Structure and Biosynthesis of Crocagins: Polycyclic Posttranslationally Modified Ribosomal Peptides from Chondromyces crocatus

Secondary metabolome mining efforts in the myxobacterial multiproducer of natural products, Chondromyces crocatus Cm c5, resulted in the isolation and structure elucidation of crocagins, which are novel polycyclic peptides containing a tetrahydropyrrolo[2,3-b]indole core. The gene cluster was identified through an approach combining genome analysis, targeted gene inactivation in the producer, and in vitro experiments. Based on our findings, we developed a biosynthetic scheme for crocagin biosynthesis. These natural products are formed from the three C-terminal amino acids of a precursor peptide and thus belong to a novel class of ribosomally synthesized and post-translationally modified peptides (RiPPs). We demonstrate that crocagin A binds to the carbon storage regulator protein CsrA, thereby inhibiting the ability of CsrA to bind to its cognate RNA target.     

Cu(i) catalysis for selective condensation/bicycloaromatization of two different arylalkynes: direct and general construction of functionalized C–N axial biaryl compounds

Selective condensation/bicycloaromatization of two different arylalkynes is firstly developed under ligand-free copper(i)-catalysis, which allows the direct synthesis of C–N axial biaryl compounds in high yields with excellent selectivity and functional group tolerance. Due to the critical effects of Cu(i) catalyst and HFIP, many easily occurring undesired reactions are suppressed, and the coupled five–six aromatic rings are constructed via the selective formation of two C(sp²)–N(sp²) bonds and four C(sp²)–C(sp²) bonds. The achievement of moderate enantioselectivity verifies its potential for the simplest asymmetric synthesis of atropoisomeric biaryls. Western blotting demonstrated that the newly developed compounds are promising targets in biology and pharmaceuticals. This unique reaction can construct structurally diverse C–N axial biaryl compounds that have never been reported by other methods, and might be extended to various applications in materials, chemistry, biology, and pharmaceuticals.

Selective condensation/bicycloaromatization of two different arylalkynes is firstly developed under ligand-free copper(i)-catalysis, which allows the direct synthesis of C–N axial biaryl compounds in high yields with excellent selectivity and functional group tolerance.     

Discovery and biosynthesis of guanipiperazine from a NRPS-like pathway

Nonribosomal peptide synthetases (NRPSs) are modular enzymes that use a thiotemplate mechanism to assemble the peptide backbones of structurally diverse and biologically active natural products in bacteria and fungi. Unlike these canonical multi-modular NRPSs, single-module NRPS-like enzymes, which lack the key condensation (C) domain, are rare in bacteria, and have been largely unexplored to date. Here, we report the discovery of a gene cluster (gup) encoding a NRPS-like megasynthetase through genome mining. Heterologous expression of the gup cluster led to the production of two unprecedented alkaloids, guanipiperazines A and B. The NRPS-like enzyme activates two l-tyrosine molecules, reduces them to the corresponding amino aldehydes, and forms an unstable imine product. The subsequent enzymatic reduction affords piperazine, which can be morphed by a P450 monooxygenase into a highly strained compound through C–O bond formation. Further intermolecular oxidative coupling forming the C–C or C–O bond is catalyzed by another P450 enzyme. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products.

Genome mining of a NRPS-like gene cluster led to the identification of two novel alkaloids with antimicrobial activity. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products.     

Ni(0)-promoted activation of Csp2–H and Csp2–O bonds

A dinickel(0)–N₂ complex, stabilized with a rigid acridane-based PNP pincer ligand, was studied for its ability to activate C(sp²)–H and C(sp²)–O bonds. Stabilized by a Ni–μ–N₂–Na⁺ interaction, it activates C–H bonds of unfunctionalized arenes, affording nickel–aryl and nickel–hydride products. Concomitantly, two sodium cations get reduced to Na(0), which was identified and quantified by several methods. Our experimental results, including product analysis and kinetic measurements, strongly suggest that this C(sp²)–H activation does not follow the typical oxidative addition mechanism occurring at a low-valent single metal centre. Instead, via a bimolecular pathway, two powerfully reducing nickel ions cooperatively activate an arene C–H bond and concomitantly reduce two Lewis acidic alkali metals under ambient conditions. As a novel synthetic protocol, nickel(ii)–aryl species were directly synthesized from nickel(ii) precursors in benzene or toluene with excess Na under ambient conditions. Furthermore, when the dinickel(0)–N₂ complex is accessed via reduction of the nickel(ii)–phenyl species, the resulting phenyl anion deprotonates a C–H bond of glyme or 15-crown-5 leading to C–O bond cleavage, which produces vinyl ether. The dinickel(0)–N₂ species then cleaves the C(sp²)–O bond of vinyl ether to produce a nickel(ii)–vinyl complex. These results may provide a new strategy for the activation of C–H and C–O bonds mediated by a low valent nickel ion supported by a structurally rigidified ligand scaffold.

A structurally rigidified nickel(0) complex was found to be capable of cleaving both C(sp²)–H and C(sp²)–O bonds.     

Ribosomally Synthesized and Post‐Translationally Modified Peptide Natural Products: New Insights into the Role of Leader and Core Peptides during Biosynthesis

Ribosomally synthesized and post‐translationally modified peptides (RiPPs) are a major class of natural products with a high degree of structural diversity and a wide variety of bioactivities. Understanding the biosynthetic machinery of these RiPPs will benefit the discovery and development of new molecules with potential pharmaceutical applications. In this Concept article, we discuss the features of the biosynthetic pathways to different RiPP classes, and propose mechanisms regarding recognition of the precursor peptide by the post‐translational modification enzymes. We propose that the leader peptides function as allosteric regulators that bind the active form of the biosynthetic enzymes in a conformational selection process. We also speculate how enzymes that generate polycyclic products of defined topologies may have been selected for during evolution.     

Iridium(I)-Catalyzed Isoindolinone-Directed Branched-Selective Aromatic C–H Alkylation with Simple Alkenes

We report an iridium(I)-catalyzed branched-selective C–H alkylation of N-arylisoindolinones with simple alkenes as the alkylating agents. The amide carbonyl group of the isoindolinone motif acts as the directing group to assist the ortho C–H activation of the N-aryl ring. With this atom-economic and highly branched-selective protocol, an array of biologically relevant N-arylisoindolinones were obtained in good yields. Asymmetric control was achieved with up to 87:13 er when a BiPhePhos-like chiral ligand was employed.     

Discovery of daspyromycins A and B, 2-aminovinyl-cysteine containing lanthipeptides,through a genomics-based approach

Lanthipeptides are one of the largest groups of ribosomally synthesized and post-translationally modified peptides(RiPPs) and are characterized by the presence of lanthionine(Lan) or methyllanthionine residues(MeLan). Only very few lanthipeptides contain a C-terminal 2-aminovinyl-cysteine(AviCys) motif, but all of them show potent antibacterial activities. Recent advances of genome sequencing led to the rapid accumulation of new biosynthetic gene clusters(BGCs) for lanthipeptides. In this study,...     

Stoichiometric to catalytic reactivity of the aryl cycloaurated species with arylboronic acids: insight into the mechanism of gold-catalyzed oxidative C(sp2)–H arylation

Based on the well-defined five-membered aryl gold(iii) complexes, [Au(tpy)X₂] (3a and 3b) and [AuBr(Ph)(tpy)] (7), as well as the aryl gold(iii) complex [AuCl₂(Ph)(tpy)] (8) (tpy = 2-(o-tolyl)pyridine) as reliable models, we present a detailed study of the mechanism for gold(iii)-catalyzed oxidative cross-coupling reactions between cycloaurable arenes and arylboronic acids. Here we report the direct evidence for a mechanistic proposal including arene C–H activation, transmetallation and biaryl reductive elimination. The chelation-assisted C–H activation strategy has been used for the development of the gold(iii)-catalyzed C–H bond arylation of arenes with aryl reagents to forge extended π-conjugated systems.     

Enantioselective total synthesis of parnafungin A1 and 10a-epi-hirtusneanine

The first and enantioselective total synthesis of the heterodimeric biaryl antifungal natural product parnafungin A1 as well as complex biaryl tetrahydroxanthone 10a-epi-hirtusneanine is accomplished, by employing cross-coupling through the benzoxaborole strategy to construct their sterically hindered biaryl cores. Besides the powerful Suzuki–Miyaura cross-coupling, the synthesis of parnafungin A1 also features a highly diastereoselective oxa-Michael addition to construct a tetrahydroxanthone skeleton, and an effective Zn-mediated reductive cyclization-Mitsunobu sequence to furnish the isoxazolidinone structure. Key innovations in total synthesis of 10a-epi-hirtusneanine include the employment of DTBS protection for functional group manipulation on the tetrahydroxanthone skeleton, stereoselective methylations, and complete reversal of the stereochemistry of the C5-hydroxy group using oxidation/Evans–Saksena reduction, as well as the strategy of preparing both complex tetrahydroxanthone monomers from the same chiral intermediate 25.

The first, enantioselective total synthesis of the heterodimeric biaryl antifungal natural product parnafungin A1 as well as 10a-epi-hirtusneanine is accomplished, using a cross-coupling strategy to construct their sterically hindered biaryl cores.     

Cobalt-catalyzed intramolecular decarbonylative coupling of acylindoles and diarylketones through the cleavage of C–C bonds

We report here cobalt–N-heterocyclic carbene catalytic systems for the intramolecular decarbonylative coupling through the chelation-assisted C–C bond cleavage of acylindoles and diarylketones. The reaction tolerates a wide range of functional groups such as alkyl, aryl, and heteroaryl groups, giving the decarbonylative products in moderate to excellent yields. This transformation involves the cleavage of two C–C bonds and formation of a new C–C bond without the use of noble metals, thus reinforcing the potential application of decarbonylation as an effective tool for C–C bond formation.

A method for cobalt–N-heterocyclic carbene catalytic systems for the intramolecular decarbonylative coupling of ketones was achieved.     

Forwards and backwards – synthesis of Laurencia natural products using a biomimetic and retrobiomimetic strategy incorporating structural reassignment of laurefurenynes C–F

Laurefurenynes C–F are four natural products isolated from Laurencia species whose structures were originally determined on the basis of extensive nuclear magnetic resonance experiments. On the basis of a proposed biogenesis, involving a tricyclic oxonium ion as a key intermediate, we have reassigned the structures of these four natural products and synthesized the four reassigned structures using a biomimetic approach demonstrating that they are the actual structures of the natural products. In addition, we have developed a synthesis of the enantiomers of the natural products laurencin and deacetyllaurencin from the enantiomer of (E)-laurefucin using an unusual retrobiomimetic strategy. All of these syntheses have been enabled by the use of tricyclic oxonium ions as pivotal synthetic intermediates.

The synthesis and structural reassignment of laurefurenynes C–F has been achieved, with the new structures fitting with a proposed biosynthesis. Also reported is the synthesis of ent-laurencin and ent-deacetyllaurencin via a retrobiomimetic approach.     

Zinc catalysed electrophilic C–H borylation of heteroarenes

Cationic zinc Lewis acids catalyse the C–H borylation of heteroarenes using pinacol borane (HBPin) or catechol borane (HBCat). An electrophile derived from [IDippZnEt][B(C₆F₅)₄] (IDipp = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) combined with N,N-dimethyl-p-toluidine (DMT) proved the most active in terms of C–H borylation scope and yield. Using this combination weakly activated heteroarenes, such as thiophene, were amenable to catalytic C–H borylation using HBCat. Competition reactions show these IDipp–zinc cations are highly oxophilic but less hydridophilic (relative to B(C₆F₅)₃), and that borylation proceeds via activation of the hydroborane (and not the heteroarene) by a zinc electrophile. Based on DFT calculations this activation is proposed to proceed by coordination of a hydroborane oxygen to the zinc centre to generate a boron electrophile that effects C–H borylation. Thus, Lewis acid binding to oxygen sites of hydroboranes represents an under-developed route to access reactive borenium-type electrophiles for C–H borylation.

Cationic zinc Lewis acids catalyse the C–H borylation of heteroarenes using pinacol borane (HBPin) or catechol borane (HBCat).     

Direct amidation of metallaaromatics: access to N-functionalized osmapentalynes via a 1,5-bromoamidated intermediate

The direct C–H amidation or imidation of metallaaromatics with N-bromoamides or imides has been achieved under mild conditions and leads to the formation of a family of N-functionalized metallapentalyne derivatives. A unique 1,5-bromoamidated species has been identified, and can be viewed as a σ^H-adduct intermediate in a nucleophilic aromatic substitution. The 1,5-addition of both electrophilic and nucleophilic moieties into the metallaaromatic framework demonstrates a novel pathway in contrast to the typical radical process of arene C–H amidation involving N-haloamide reagents.

The direct C–H amidation of metallapentalyne has been achieved under mild conditions in which key 1,5-bromoamidated intermediates was determined.     

Studies on the Synthesis of Indothiazinone and Its Derivatives via Direct 3-Acylation of Indole

Indothiazinone is a natural 3-acylindole alkaloid, isolated from a culture of myxobacterial strain. It was found to possess antibacterial activity against yeast and filamentous fungi. Indothiazinone is also structurally related with a mammalian endogenous aryl hydrocarbon receptor ligand, (2-(1′H-indole-3′-carbonyl)thiazol-4-carboxylic acid methyl ester (ITE). In this article, the synthesis of indothiazinone has been disclosed for the first time. Key feature includes direct and selective 3-acylation of indole in the presence of Lewis acid. In addition, an efficient preparation of N-substituted indothiazinone derivatives has been demonstrated.     

Substrate specificity and reaction directionality of a three-residue cyclophane forming enzyme PauB

Three-residue cyclophane-forming enzymes (3-CyFEs) are a group of radical S-adenosylmethionine (SAM) enzymes involved in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs). 3-CyFE catalyzes the crosslinking between an aromatic residue (Ω1) and a non-aromatic residue (X3) in a Ω1-X2-X3 motif to produce a cyclophane ring, a key step in the biosynthesis of the RiPP natural product triceptide. In this study, we perform a genome-wide search for the Xye-type triceptides, showing these RiPPs are likely class-specific and only present in gamma-proteobacteria. The 3-CyFE PauB from Photorhabdus australis exhibits a relaxed substrate specificity on the X3 position, but glycine in this position is not suitable for cyclophane formation. We also reconstituted the activity of PauB in vitro, showing it produces the N-terminal cyclophane firstly, and then the C-terminal ring, whereas the middle cyclophane is produced in the last step.     

Exploring the biosynthetic potential of bimodular aromatic polyketide synthases

Polycyclic aromatic polyketides such as actinorhodin and tetracenomycin are synthesized from acetate equivalents by type II polyketide synthases (PKS). Their carbon chain backbones are derived from malonyl-CoA building blocks through the action of a minimal PKS module consisting of a ketosynthase, a chain length factor, an acyl carrier protein (ACP) and a malonyl-CoA/ACP transacylase. In contrast to these acetogenic polyketides, the backbones of a few aromatic polyketide natural products, such as the R1128 antibiotics, are primed by non-acetate building blocks. These polyketides are synthesized by bimodular PKSs comprising of a dedicated initiation module, which includes a ketosynthase, acyl transferase and ACP, as well as a minimal PKS module. Recently we showed that regioselectively modified polyketides could be synthesized through the genetic recombination of initiation modules and minimal PKS modules from different polyketide biosynthetic pathways (Tang et al. PLoS Biol. 2004, 2, 227-238). For example, the actinorhodin and tetracenomycin minimal PKSs could accept and elongate unnatural primer units from the R1128 initiation module. In this report we provide further examples of using heterologous bimodular PKSs for the engineered biosynthesis of new aromatic polyketides. In addition to providing insights into the biosynthetic mechanisms of aromatic PKSs, our findings also highlight considerable potential for crosstalk between amino acid catabolism and aromatic polyketide biosynthesis. For example, exogenously supplied unnatural amino acids are efficiently incorporated into bioactive anthraquinone antibiotics.     

Synthesis of chiral linear and macrocyclic candidates: VI. Synthesis and antibacterial activity of some macrocyclic tripeptides and linear dipeptide Schiff bases

A series of macrocyclic tripeptides and linear dipeptide Schiff base derivatives has been synthesized using pyridine-3,5-dicarboxylic acid and L-phenyalanine methyl ester as starting materials. Treatment of pyridine-3,5-dicarbonyl dichloride with L-phenylalanine methyl ester gave N,N′-(pyridine-3,5-diyldicarbonyl)bis(L-phenyalanine methyl ester) which was hydrolyzed with 1N sodium hydroxide to the corresponding bis-acid, and the latter was cyclized with diamino acids to afford macrocyclic tripeptide derivatives. The reaction of the bis ester with hydrazine hydrate gave bis-hydrazide, which was condensed with aldehydes to obtain the corresponding Schiff base derivatives. The structures of the newly synthesized compounds were confirmed by IR, ¹H and ¹³C NMR, and MS spectral data and elemental analyses. The antimicrobial activities of some of the newly synthesized compounds were comparable with that of Streptomycin used as control.     

Can acyclic conformational control be achieved via a sulfur–fluorine gauche effect?

The gauche conformation of the 1,2-difluoroethane motif is known to involve stabilising hyperconjugative interactions between donor (bonding, σ_C–H) and acceptor (antibonding, σ*C–F) orbitals. This model rationalises the generic conformational preference of F–C_β–C_α–X systems (φ_FCCX ≈ 60°), where X is an electron deficient substituent containing a Period 2 atom. Little is known about the corresponding Period 3 systems, such as sulfur and phosphorus, where multiple oxidation states are possible. Conformational analyses of β-fluorosulfides, -sulfoxides and -sulfones are disclosed here, thus extending the scope of the fluorine gauche effect to the 3rd Period (F–C–C–S(O)_n; φ_FCCS ≈ 60°). Synergy between experiment and computation has revealed that the gauche effect is only pronounced in structures bearing an electropositive vicinal sulfur atom (S⁺–O^–, SO₂).     

Ruthenium-catalyzed cascade C–H activation/annulation of N-alkoxybenzamides: reaction development and mechanistic insight

A highly selective ruthenium-catalyzed C–H activation/annulation of alkyne-tethered N-alkoxybenzamides has been developed. In this reaction, diverse products from inverse annulation can be obtained in moderate to good yields with high functional group compatibility. Insightful experimental and theoretical studies indicate that the reaction to the inverse annulation follows the Ru(ii)–Ru(iv)–Ru(ii) pathway involving N–O bond cleavage prior to alkyne insertion. This is highly different compared to the conventional mechanism of transition metal-catalyzed C–H activation/annulation with alkynes, involving alkyne insertion prior to N–O bond cleavage. Via this pathway, the in situ generated acetic acid from the N–H/C–H activation step facilitates the N–O bond cleavage to give the Ru-nitrene species. Besides the conventional mechanism forming the products via standard annulation, an alternative and novel Ru(ii)–Ru(iv)–Ru(ii) mechanism featuring N–O cleavage preceding alkyne insertion has been proposed, affording a new understanding of transition metal-catalyzed C–H activation/annulation.

A highly selective ruthenium-catalyzed C–H activation/annulation through a pathway involving N–O bond cleavage prior to alkyne insertion is developed.     

Discovery and characterisation of an amidine-containing ribosomally-synthesised peptide that is widely distributed in nature

Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural product with a wide range of bioactivities. Genome mining for RiPP biosynthetic gene clusters (BGCs) is often hampered by poor annotation of the short precursor peptides that are ultimately modified into the final molecule. Here, we utilise a previously described genome mining tool, RiPPER, to identify novel RiPP precursor peptides near YcaO-domain proteins, enzymes that catalyse various RiPP post-translational modifications including heterocyclisation and thioamidation. Using this dataset, we identified a novel and diverse family of RiPP BGCs spanning over 230 species of Actinobacteria and Firmicutes. A representative BGC from Streptomyces albidoflavus J1074 (formerly known as Streptomyces albus) was characterised, leading to the discovery of streptamidine, a novel amidine-containing RiPP. This new BGC family highlights the breadth of unexplored natural products with structurally rare features, even in model organisms.

Genome mining for pathways containing YcaO proteins revealed a widespread novel family of RiPP gene clusters. A model gene cluster was characterised through genetic and chemical analyses, which yielded streptamidine, a novel amidine-containing RiPP.