Discovery of a Cryptic Nitro Intermediate in the Biosynthesis of the 3-(trans-2'-Aminocyclopropyl)alanine Moiety of Belactosin A

Discovery of Noncanonical Iron and 2-Oxoglutarate Dependent Enzymes Involved in C-C and C-N Bond Formation in Biosynthetic Pathways

Iron and 2-oxoglutarate dependent (Fe/2OG) enzymes utilize an FeIV=O species to catalyze the functionalization of otherwise chemically inert C-H bonds. In addition to the more familiar canonical reactions of hydroxylation and chlorination, they also catalyze several other types of reactions that contribute to the diversity and complexity of natural products. In the past decade, several new Fe/2OG enzymes that catalyze C-C and C-N bond formation have been reported in the biosynthesis of structurally complex natural products. Compared with hydroxylation and chlorination, the catalytic cycles of these Fe/2OG enzymes involve distinct mechanistic features to enable noncanonical reaction outcomes. This Review summarizes recent discoveries of Fe/2OG enzymes involved in C-C and C-N bond formation with a focus on reaction mechanisms and their roles in natural product biosynthesis.

Nitrocyclopropanes as Valuable Building Blocks in Organic Synthesis and Biology: Exploring the Origin of the Nitro Group

Cyclopropane derivatives serve as important building blocks in organic synthesis, due to their three-membered stretched ring. Nitro-substituted cyclopropanes (NCPs) represent a special class of donor-acceptor cyclopropanes (DACs) that contain a strong electron-withdrawing nitro group as substituent on the cyclopropyl moiety. Due to the versatile nature of the nitro group, which can be converted into other functional azo groups or heterocyclic scaffolds, NCPs are considered important building blocks in the design of complex organic compounds. Herein, the present review is organized in two main sections focused on the synthesis and application of NCPs. The part containing the synthetic methodologies of NCPs has been further divided into distinct sections based mainly on the nature of the starting materials, such as: a) from nitroalkenes, b) from nitro-bearing diazo compounds, c) from nitroalkanes in combination with alkenes, d) from aminocyclopropanes under oxidative conditions, and e) from various nitro compounds, through miscellaneous processes. In the part concerning the applications and use of NCPs, the categorization includes three main subcategories, concerning their reduction to 1-aminocyclopropane-1-carboxylic acids (ACC), the ring opening of NCPs leading to valuable open-chain heterocycles, and the ring expansion to larger cyclic and heterocyclic compounds.

Biocatalytic Strategies for Nitration Reactions

Nitro compounds are key synthetic intermediates used as enabling tools in synthesis and found in a large range of essential compounds, including pharmaceuticals, pesticides, and various organic dyes. Despite recent methodological developments, the industrial preparation of nitro compounds still suffers from harsh reaction conditions, along with poor selectivity and a problematic environmental footprint. Although biological enzymatic methods exist, mild approaches for bionitration are still underexplored. Enzymes, with their exquisite selectivity and compatibility with mild reaction conditions, have the potential to revolutionize the way nitro compounds are prepared. In this perspective, we systematically analyze currently available biological/enzymatic methods, including the oxidation of an amine precursor or methods consisting of direct oxidative nitration and non-oxidative nitration. By examining both the scope and mechanism of these reactions, we aim to present an update on the state-of-the-art while highlighting current challenges in this emerging field. The goal of this perspective is to inspire innovation in enzymatic nitration for sustainable organic synthesis, providing chemists with a valuable guide.

Cryptic enzymatic assembly of peptides armed with β-lactone warheads

Nature has evolved biosynthetic pathways to molecules possessing reactive warheads that inspired the development of many therapeutic agents, including penicillin antibiotics. Peptides armed with electrophilic warheads have proven to be particularly effective covalent inhibitors, providing essential antimicrobial, antiviral and anticancer agents. Here we provide a full characterization of the pathways that nature deploys to assemble peptides with β-lactone warheads, which are potent proteasome inhibitors with promising anticancer activity. Warhead assembly involves a three-step cryptic methylation sequence, which is likely required to reduce unfavorable electrostatic interactions during the sterically demanding β-lactonization. Amide-bond synthetase and adenosine triphosphate (ATP)-grasp enzymes couple amino acids to the β-lactone warhead, generating the bioactive peptide products. After reconstituting the entire pathway to β-lactone peptides in vitro, we go on to deliver a diverse range of analogs through enzymatic cascade reactions. Our approach is more efficient and cleaner than the synthetic methods currently used to produce clinically important warhead-containing peptides.

Characterization of Aziridine-Forming α-Ketoglutarate-Dependent Oxygenase in l-Isovaline Biosynthesis

l-Isovaline biosynthesis by TqaLFM-ti from Tolypocladium inflatum was demonstrated in vitro. The biochemical analysis of the α-ketoglutarate-dependent oxygenase TqaL-ti revealed that it produces (2S,3S)-3-ethyl-3-methylaziridine-2-carboxylic acid from l-isoleucine, thus exhibiting a stereoselectivity different from those of the reported homologues. Remarkably, a single mutation on I295 in TqaL-ti completely exchanged its stereoselectivity to produce the C-3 stereoisomer. TqaFM-ti generates d-isovaline from (2S,3R)-aziridine-2-carboxylic acid, suggesting that the stereochemistry of the TqaL product defines that of isovaline.

Characterization of the cystargolide biosynthetic gene cluster and functional analysis of the methyltransferase CysG

Cystargolides are natural products originally isolated from Kitasatospora cystarginea NRRL B16505 as inhibitors of the proteasome. They are composed of a dipeptide backbone linked to a β-lactone warhead. Recently, we identified the cystargolide biosynthetic gene cluster, but systematic genetic analyses had not been carried out because of the lack of a heterologous expression system. Here, we report the discovery of a homologous cystargolide biosynthetic pathway in Streptomyces durhamensis NRRL-B3309 by genome mining. The gene cluster was cloned via transformation-associated recombination and heterologously expressed in Streptomyces coelicolor M512. We demonstrate that it contains all genes necessary for the production of cystargolide A and B. Single gene deletion experiments reveal that only five of the eight genes from the initially proposed gene cluster are essential for cystargolide synthesis. Additional insights into the cystargolide pathway could be obtained from in vitro assays with CysG and chemical complementation of the respective gene knockout. This could be further supported by the in vitro investigation of the CysG homolog BelI from the belactosin biosynthetic gene cluster. Thereby, we confirm that CysG and BelI catalyze a cryptic SAM-dependent transfer of a methyl group that is critical for the construction of the cystargolide and belactosin β-lactone warheads.

Unusual Enzymatic C-C Bond Formation and Cleavage Reactions during Natural Product Biosynthesis

Natural products from plants and microorganisms provide a valuable reservoir of pharmaceutical compounds. C-C bond formation and cleavage are crucial events during natural product biosynthesis, playing pivotal roles in generating diverse and intricate chemical structures that are essential for biological functions. This review summarizes our recent findings regarding biosynthetic enzymes that catalyze unconventional C-C bond formation and cleavage reactions during natural product biosynthesis.

Three-membered ring formation catalyzed by α-ketoglutarate-dependent nonheme iron enzymes

Epoxides, aziridines, and cyclopropanes are found in various medicinal natural products, including polyketides, terpenes, peptides, and alkaloids. Many classes of biosynthetic enzymes are involved in constructing these ring structures during their biosynthesis. This review summarizes our current knowledge regarding how α-ketoglutarate-dependent nonheme iron enzymes catalyze the formation of epoxides, aziridines, and cyclopropanes in nature, with a focus on enzyme mechanisms.

Tigliane Diterpenoids

The distribution, chemistry, and molecular bioactivity of tiglianes are reviewed from the very beginning of the studies on these diterpenoids, summarizing their clinical and toxicological literature mostly in its more recent and controversial aspects, and critically analyzing various proposals for their biosynthesis.

Mechanistic Analysis of Stereodivergent Nitroalkane Cyclopropanation Catalyzed by Nonheme Iron Enzymes

BelL and HrmJ are α-ketoglutarate-dependent nonheme iron enzymes that catalyze the oxidative cyclization of 6-nitronorleucine, resulting in the formation of two diastereomeric 3-(2-nitrocyclopropyl)alanine (Ncpa) products containing trans-cyclopropane rings with (1'R,2'R) and (1'S,2'S) configurations, respectively. Herein, we investigate the catalytic mechanism and stereodivergency of the cyclopropanases. The results suggest that the nitroalkane moiety of the substrate is first deprotonated to produce the nitronate form. Spectroscopic analyses and biochemical assays with substrates and analogues indicate that an iron(IV)-oxo species abstracts proS-H from C4 to initiate intramolecular C-C bond formation. A hydroxylation intermediate is unlikely to be involved in the cyclopropanation reaction. Additionally, a genome mining approach is employed to discover new homologues that perform the cyclopropanation of 6-nitronorleucine to generate cis-configured Ncpa products with (1'R,2'S) or (1'S,2'R) stereochemistries. Sequence and structure comparisons of these cyclopropanases enable us to determine the amino acid residues critical for controlling the stereoselectivity of cyclopropanation.

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

BACKGROUND

Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva.

RESULTS

We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously.

CONCLUSIONS

Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo. Video Abstract.

Oxidative modification of free-standing amino acids by Fe(II)/αKG-dependent oxygenases

Fe(II)/α-ketoglutarate (αKG)-dependent oxygenases catalyze the oxidative modification of various molecules, from DNA, RNA, and proteins to primary and secondary metabolites. They also catalyze a variety of biochemical reactions, including hydroxylation, halogenation, desaturation, epoxidation, cyclization, peroxidation, epimerization, and rearrangement. Given the versatile catalytic capability of such oxygenases, numerous studies have been conducted to characterize their functions and elucidate their structure-function relationships over the past few decades. Amino acids, particularly nonproteinogenic amino acids, are considered as important building blocks for chemical synthesis and components for natural product biosynthesis. In addition, the Fe(II)/αKG-dependent oxygenase superfamily includes important enzymes for generating amino acid derivatives, as they efficiently modify various free-standing amino acids. The recent discovery of new Fe(II)/αKG-dependent oxygenases and the repurposing of known enzymes in this superfamily have promoted the generation of useful amino acid derivatives. Therefore, this study will focus on the recent progress achieved from 2019 to 2022 to provide a clear view of the mechanism by which these enzymes have expanded the repertoire of free amino acid oxidative modifications.

Diastereoselective and Enantioselective Synthesis of α-p-Methoxyphenoxy-β-Lactones: Dependence on the Stereoelectronic Properties of the β-Hydroxy-α-p-Methoxyphenoxycarboxylic Acid Precursors

Treatment of β-hydroxy-α-p-methoxyphenoxy carboxylic acids derived from the asymmetric glycolate aldol addition reaction with p-nitrobenzenesulfonyl chloride yielded divergent results depending on the nature of the β-substituent of the carboxylic acid. Substrates bearing either alkyl substituents (R = -n-butyl, -n-octyl, -benzyl, isopropyl, -tert-butyl) or aryl systems bearing electron-withdrawing substituents (R = -p-C₆H₄Cl, -p-C₆H₄Br, -p-C₆H₄NO₂) yielded β-lactones. In contrast, α-p-methoxyphenoxy-β-hydroxycarboxylic acids bearing electron-donating aryl groups or the sterically demanding 2-naphthyl group formed (Z)-alkenes.

Hot off the Press

A personal selection of 32 recent papers is presented, covering various aspects of current developments in bioorganic chemistry and novel natural products, such as daphnepapytone A from Daphne papyracea.