Biosynthesis of alkyne-containing natural products

Enediyne natural product biosynthesis unified by a diiodotetrayne intermediate

Enediyne natural products are renowned for their potent cytotoxicities but the biosynthesis of their defining 1,5-diyne-3-ene core moiety remains largely enigmatic. Since the discovery of the enediyne polyketide synthase cassette in 2002, genome sequencing has revealed thousands of distinct enediyne biosynthetic gene clusters, each harboring the conserved enediyne polyketide synthase cassette. Here we report that (1) the products of this cassette are an iodoheptaene, a diiodotetrayne and two pentaynes; (2) the diiodotetrayne represents a common biosynthetic intermediate for all known enediynes; and (3) cryptic iodination can be exploited to increase enediyne titers. These findings establish a unified biosynthetic pathway for the enediynes, set the stage to further advance enediyne core biosynthesis and enable fundamental breakthroughs in chemistry, enzymology and translational applications of enediyne natural products.

Indium(III)-Catalyzed Haloalkynylation Reaction of Alkynes

Green chemistry strives for sustainability at the molecular level and is gaining increasing relevance in the development of chemical reactions. The haloalkynylation reaction is a highly atom-economical C-C coupling reaction that was previously only achieved using transition metal catalysts. It enables the introduction of an alkyne unit and a halogen atom into the target molecule. Herein, we present a haloalkynylation reaction catalyzed by indium(III) halides. The use of indium(III) bromide as a catalyst leads exclusively to the cis addition products with yields up to 86 %. In addition, iodoacetylenes can be applied for the first time for the haloalkynylation reaction of internal alkynes which is an important step forward in the development of industrially relevant and sustainable catalysts. In contrast to gold catalysis, which proceeds via a similar mechanism, the use of alkyl-substituted haloacetylenes as reagents is also possible. Based on 13C labeling experiments and quantum chemical calculations, we postulate two possible mechanisms for the indium(III)-catalyzed haloalkynylation reactions.

Protocol for Sonogashira coupling of alkynes and aryl halides via nickel catalysis

Alkynes are widely present in natural products and pharmaceutical compounds. Here, we present a protocol for nickel-catalyzed cross-coupling of terminal alkynes with aryl iodides or bromides for constructing a C(sp2)-C(sp) bond. We describe steps for reagent preparation, reaction setup, purification process, and product characterization. We also detail procedures for obtaining a single crystal of 6-(phenylethynyl)-1-(phenylsulfonyl)-1H-indole (3b). The application of this protocol is limited to aryl bromide and iodide. For complete details on the use and execution of this protocol, please refer to Chen et al.1.

Pd(II)-Catalyzed β-C(sp3)-H Alkynylation of Alanine in Di- and Tripeptides with Asn as an Endogenous Directing Group

The introduction of alkyne moieties into peptides remains in demand as it represents a promising approach for further structural diversification of peptides. Herein, we describe the Pd(II)-catalyzed C(sp3)-H alkynylation of Ala-Asn-embedded di- and tripeptides using Asn as the endogenous lead group. In addition, a key building block for the glycopeptide Tyc4PG-14 and Tyc4PG-15 was produced by our methodology.

Anti-inflammatory acetylenic meroterpenoids from the ascidian-derived fungus Amphichorda felina SYSU-MS7908

A combination strategy of 13C NMR and bioinformatics was established to expedite the discovery of acetylenic meroterpenoids from the ascidian-derived fungus Amphichorda felina SYSU-MS7908. This approach led to the identification of 13 acetylenic meroterpenoids (1-13) and four biogenic analogs (14-17), including five new ones named felinoids A-E (1-4 and 15). Their structures and absolute configurations were elucidated using extensive spectroscopy, ECD quantum chemical calculations, and single-crystal X-ray diffraction analysis. Compound 1 possessed a rare cyclic carbonate in natural acetylenic meroterpenoids. The plausible shikimate-terpenoid biosynthetic pathways of 1-4 were also postulated. Five of these isolates exhibited anti-inflammatory activity by inhibiting NO production in LPS-induced RAW264.7 cells (IC50 = 11.6-19.5 μM). Moreover, oxirapentyn E diacetate showed a dose-dependent inhibition of pro-inflammatory cytokines IL-6 and TNF-α. Structural modification of oxirapentyn B yielded 29 new derivatives, among which seven showed improved activity (IC50 < 3 μM) and higher selectivity index (SI > 22). The structure-activity relationship study indicated that 7, 8-epoxy, and 6-acylation were crucial for the activity. These findings may provide a powerful tool to accelerate the discovery of new fungal acetylenic meroterpenoids for future anti-inflammatory drug development.

1,3-Diynes: A Versatile Precursor in Transition-Metal Catalyzed (Mediated) C-H Functionalizations

Transition metal-catalyzed C-H functionalization of diverse arenes with alkyne units has attracted enormous attention for decades since they provide straightforward access to various functionalization/annulations, which are commonly present in bioactive compounds and natural products. Recently, conjugated alkynes (1,3-diynes) have been utilized as key coupling partner in many C-H activation reactions due to their versatile characteristic properties. The presence of two C≡C bonds in conjugated 1,3-diyne brings the new diversity in synthetic transformations, such as chemo-, regioselective pathways, mono-bis functionalizations, cascade annulations, etc. Herein, we summarized the latest developments in the realm of transition-metal-catalyzed C-H functionalizations of diverse arenes with 1,3-diynes. Moreover, we highlighted the diverse transformations, conditions, mechanisms and applications of the corresponding reaction in detail.

Copper-Catalyzed Synthesis of Difluoromethyl Alkynes from Terminal and Silyl Acetylenes

An efficient method for the direct C(sp)-H difluoromethylation of terminal alkynes and the desilylation-difluoromethylation of (trimethylsilyl)acetylenes is disclosed. The copper-catalyzed transformation provides access to a wide range of structurally diverse CF₂H alkynes in good yields, utilizing a (difluoromethyl)zinc reagent and an organic oxidant. The difluoromethylation of important synthons and API's is showcased. The synthetic utility of these (difluoromethyl)alkynes is demonstrated by selected cycloaddition reactions. Additionally, a slight modification to the reaction conditions allowed the selective preparation of a 2-difluoromethylindole.

The Alkyne Zipper Reaction: A Useful Tool in Synthetic Chemistry

The alkyne zipper reaction is an internal-to-terminal alkyne isomerization reaction with many interesting applications in synthetic chemistry, as it constitutes an efficient means of achieving acetylene functionalization. A review of its applications in synthesis processes is presented in this paper, with a brief overview of the mechanistic features of the alkyne zipper reaction, as well as a brief overview of its future potential.

On-DNA Alkyne Iodination and Acetylenic Coupling as a Useful Tool for DEL Synthesis

1-Iodoalkynes and 1,3-diynes are versatile chemical intermediates and pharmaceutically valuable ingredients. In this study, copper mediated on-DNA alkyne iodination and Cadiot-Chodkiewicz coupling are developed for the first time. This generates diverse, systematic, and unprecedented topographic structural features, which could be invaluable as molecular recognition agents for drug discovery in DEL screening.

Genome Mining Discovery of Protegenins A-D, Bacterial Polyynes Involved in the Antioomycete and Biocontrol Activities of Pseudomonas protegens

Some bacteria uniquely produce "bacterial polyynes", which possess a conjugated C≡C bond starting with a terminal alkyne, and use them as chemical weapons against hosts and competitors. Pseudomonas protegens Cab57, a biocontrol agent against plant pathogens, has an orphan biosynthetic gene cluster for bacterial polyynes (named protegenins). In this study, the isolation, structure elucidation, and biological characterization of protegenins A-D are reported. The structures of protegenins A-D determined by spectroscopic and chemical techniques were octadecanoic acid derivatives possessing an ene-tetrayne, ene-triyne-ene, or ene-triyne moiety. The protegenins exhibited weak to strong antioomycete activity against Pythium ultimum OPU774. The deletion of proA, a protegenin biosynthetic gene, resulted in the reduction of the antioomycete activity of P. protegens. The Gac/Rsm system, a quorum sensing-like system of Pseudomonas bacteria, regulated the production of protegenins. The production profile of protegenins was dependent on the culturing conditions, suggesting a control mechanism for protegenin production selectivity. P. protegens suppressed the damping-off of cucumber seedlings caused by P. ultimum, and this protective effect was reduced in the proA-deletion mutant. Altogether, protegenins are a new class of bacterial polyynes which contribute to the antioomycete and plant-protective effects of P. protegens.

Thiotemplated Biosynthesis of Bacterial Polyyne Fatty Acids by a Designated Desaturase Triad

Various bacterial species are capable of producing highly modified fatty acid derivatives with conjugated triple bonds, which play important ecological roles as antifungals and toxins in mutualistic and pathogenic interactions. Furthermore, the terminal polyyne moiety is of interest as pharmacophore and as tag in bioorthogonal chemistry and live imaging. To gain insight into the assembly of these highly reactive natural products, we investigated tetrayne (caryoynencin and protegencin) biosynthesis genes (cay and pgn) from Trinickia caryophylli and Pseudomonas protegens. Pathway dissection and reconstitution in the heterologous host Burkholderia graminis revealed the genes minimally required for polyyne formation. Mutational analyses and biochemical assays demonstrated that polyyne biosynthesis is thiotemplated, involving a fatty acyl-AMP ligase, a designated acyl carrier protein, and a thioesterase. Heterologous expression of point-mutated desaturase genes showed that three desaturases work synergistically to introduce four triple bonds. These findings point to an intricate desaturase complex and provide important information for future bioengineering experiments.

Variation on a theme: the structures and biosynthesis of specialized fatty acid natural products in plants

Plants are able to construct lineage-specific natural products from a wide array of their core metabolic pathways. Considerable progress has been made toward documenting and understanding, for example, phenylpropanoid natural products derived from phosphoenolpyruvate via the shikimate pathway, terpenoid compounds built using isopentyl pyrophosphate, and alkaloids generated by the extensive modification of amino acids. By comparison, natural products derived from fatty acids have received little attention, except for unusual fatty acids in seed oils and jasmonate-like oxylipins. However, scattered but numerous reports show that plants are able to generate many structurally diverse compounds from fatty acids, including some with highly elaborate and unique structural features that have novel bioproduct functionalities. Furthermore, although recent work has shed light on multiple new fatty acid natural product biosynthesis pathways and products in diverse plant species, these discoveries have not been reviewed. The aims of this work, therefore, are to (i) review and systematize our current knowledge of the structures and biosynthesis of fatty acid-derived natural products that are not seed oils or jasmonate-type oxylipins, specifically, polyacetylenic, very-long-chain, and aromatic fatty acid-derived natural products, and (ii) suggest priorities for future investigative steps that will bring our knowledge of fatty acid-derived natural products closer to the levels of knowledge that we have attained for other phytochemical classes.

Biosynthesis of Isonitrile- and Alkyne-Containing Natural Products

Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.

Alkynyl Sulfonium Salts Can Be Employed as Chalcogen-Bonding Catalysts and Generate Alkynyl Radicals under Blue-Light Irradiation

Chalcogen bonding (ChB) has emerged as a promising tool in organic synthesis. However, compared with the well-developed selenium- and tellurium-based salt catalysts, the ChB catalysis of sulfonium salts is still unknown. Here, we report a new type of alkynyl-sulfonium salt ChB catalysis for various ionic transformations, including transfer hydrogenation, bromination, bromolactonization, dimerization of 1,1-diphenylethylene, nitro-Michael addition reaction and Ritter reaction. More importantly, the photocapability of ChB was first demonstrated to generate alkynyl radicals for the synthesis of a variety of chalcogenoacetylenes. Mechanistic studies shed light on the mechanism of the photoinduced reactions and confirmed the involvement of alkynyl radicals which are difficult to generate otherwise.

Ag2O-mediated Tandem Reaction between Terminal Alkyne and o-Iodibenzoic Acid: Construction of 3-Ethylideneisobenzofuran-1(3H)-ones

Taking aryl propargyl ether and o-iodibenzoic acid as substrates, a series of aryl cyclolactones bearing an exocyclized C=C bond were constructed with moderate to good yields. Diverse substituent groups could be tolerant in the reaction, which indicated excellent compatibility of the reaction. In this tandem reaction, Ag2O was employed as the media and Et3N was screened as the base to facilitate the reaction. A concise mechanism was proposed on the basis of the expansion of the substrates and theoretical analysis. Sonogashira type coupling coupled with intramolecular nucleophilic addition in one pot to construct the product, 3-ethylideneisobenzofuran-1(3H)-one.

Cryptic halogenation reactions in natural product biosynthesis

Covering: Up to December 2020Enzymatic halogenation reactions are essential for the production of thousands of halogenated natural products. However, in recent years, scientists discovered several halogenases that transiently incorporate halogen atoms in intermediate biosynthetic molecules to activate them for further chemical reactions such as cyclopropanation, terminal alkyne formation, C-/O-alkylation, biaryl coupling, and C-C rearrangements. In each case, the halogen atom is lost in the course of biosynthesis to the final product and is hence termed "cryptic". In this review, we provide an overview of our current knowledge of cryptic halogenation reactions in natural product biosynthesis.