Total Synthesis and Computational Investigations of Sesquiterpene-Tropolones Ameliorate Stereochemical Inconsistencies and Resolve an Ambiguous Biosynthetic Relationship

Late-stage benzenoid-to-troponoid skeletal modification of the cephalotanes exemplified by the total synthesis of harringtonolide

Skeletal modifications enable elegant and rapid access to various derivatives of a compound that would otherwise be difficult to prepare. They are therefore a powerful tool, especially in the synthesis of natural products or drug discovery, to explore different natural products or to improve the properties of a drug candidate starting from a common intermediate. Inspired by the biosynthesis of the cephalotane natural products, we report here a single-atom insertion into the framework of the benzenoid subfamily, providing access to the troponoid congeners - representing the reverse of the proposed biosynthesis (i.e., a contra-biosynthesis approach). Computational evaluation of our designed transformation prompted us to investigate a Büchner-Curtius-Schlotterbeck reaction of a p-quinol methylether, which ultimately results in the synthesis of harringtonolide in two steps from cephanolide A, which we had previously prepared. Additional computational studies reveal that unconventional selectivity outcomes are driven by the choice of a Lewis acid and the nucleophile, which should inform further developments of these types of reactions.

Exploring the Chemical Space Accessed by Chiral Pool Terpenes. The (-)-Caryophyllene Oxide Paradigm

Terpenes represent a flourishing source of structural motifs that can be converted into several more complex architectures. Realization of such transformations in a concise and efficient manner adds great value to the starting material. Herein, we study the case of (-)-caryophyllene oxide and convert it into natural sesquiterpenoids (rumphellolide K, rumphellaone A, and antipacid A), thus expanding the chemical space accessed by its privilege structure. Our semisyntheses are short and rely on reagent-dictated stereo- and chemoselectivity.

Recent Advances in Chemistry and Antioxidant/Anticancer Biology of Monoterpene and Meroterpenoid Natural Product

Monoterpenes and meroterpenes are two large classes of isoprene-based molecules produced by terrestrial plants and unicellular organisms as diverse secondary metabolites. The global rising incidence of cancer has led to a renewed interest in natural products. These monoterpenes and meroterpenes represent a novel source of molecular scaffolds that can serve as medicinal chemistry platforms for the development of potential preclinical leads. Furthermore, some of these natural products are either abundant, or their synthetic strategies are scalable as it will be indicated here, facilitating their derivatization to expand their scope in drug discovery. This review is a collection of representative updates (from 2016-2023) in biologically active monoterpene and meroterpenoid natural products and focuses on the recent findings of the pharmacological potential of these bioactive compounds as well as the newly developed synthetic strategies employed to access them. Particular emphasis will be placed on the anticancer and antioxidant potential of these compounds in order to raise knowledge for further investigations into the development of potential anti-cancer therapeutics. The mounting experimental evidence from various research groups across the globe regarding the use of these natural products at pre-clinical levels, renders them a fast-track research area worth of attention.

Intramolecular Alkyne-de Mayo Reaction Using the Enol Methylene Acetal Linker: Experimental Implementation and Computational Simulation

The enol-linked intramolecular alkyne-de Mayo reaction is a photochemically triggered cascade reaction suitable for the synthesis of substituted dihydrotropones by two-carbon ring expansion of enol ethers of cyclopentane-1,3-dion. We report on the implementation of the methylene acetal linker and the isolation of the initial (2 + 2) photocycloadduct in substances. We have investigated in depth the modus operandi of the ring-opening of the π-donor-π-acceptor cyclobutene derivatives by computational chemistry.

Engineered and total biosynthesis of fungal specialized metabolites

Filamentous fungi produce a very wide range of complex and often bioactive metabolites, demonstrating their inherent ability as hosts of complex biosynthetic pathways. Recent advances in molecular sciences related to fungi have afforded the development of new tools that allow the rational total biosynthesis of highly complex specialized metabolites in a single process. Increasingly, these pathways can also be engineered to produce new metabolites. Engineering can be at the level of gene deletion, gene addition, formation of mixed pathways, engineering of scaffold synthases and engineering of tailoring enzymes. Combination of these approaches with hosts that can metabolize low-value waste streams opens the prospect of one-step syntheses from garbage.

Phosphine-catalyzed formal Buchner [6+1] annulation: de novo construction of cycloheptatrienes

An unprecedented phosphine-catalyzed formal Buchner [6+1] annulation of a newly designed allenoate has been developed, providing a series of cycloheptatriene derivatives in moderate to good yields (up to 99%). This reaction demonstrates that the introduction of an electrophilic allylic group to allenoates effectively extends the reaction scope of phosphine-catalyzed annulation, providing a concise route to cycloheptatrienes. Mechanistic study indicated that this reaction involves a [4+2] Diels-Alder reaction and ring expansion of the bicyclo[4.1.0] moiety, which is similar to the Buchner reaction. Notably, an enantioselective variant of this [6+1] annulation can also be performed using a chiral iminophosphine catalyst.

Semisynthesis of Linariophyllenes A-C and Rumphellolide H, Structure Revisions and Proposed Biosynthesis Pathways

The first semisynthetic routes toward terrestrial anti-inflammatory natural products linariophyllene A-C and the refined route toward marine natural product rumphellolide H are presented. Among the synthesized target compounds, the correct structure of linariophyllene A was determined to be the diastereomer of the originally proposed structure with an inverted stereocenter at the secondary alcohol. The proposed structures of linariophyllene B and rumphellolide H were confirmed. However, the correct structure of linariophyllene C was found to be the diastereomer of the originally proposed structure with an inverted stereocenter at the tertiary carbon of the epoxide moiety. The structures of linariophyllenes A-C and rumphellolide H were unequivocally confirmed by single-crystal X-ray diffractometry. The obtained results enabled the proposal of the biosynthetic origins of the aforementioned natural products and bolstered the diversity of available sesquiterpenoids. Linariophyllenes A-C and rumphellolide H were obtained in sufficient amounts to further expand their bioactivity profile and utility as reference standards in future studies of chemical constituents of terrestrial and marine organisms.

Tandem intermolecular [4 + 2] cycloadditions are catalysed by glycosylated enzymes for natural product biosynthesis

Tandem Diels-Alder reactions are frequently used in the construction of polycyclic ring systems in complex organic compounds. Unlike the many Diels-Alderases (DAases) that catalyse a single cycloaddition, enzymes for multiple Diels-Alder reactions are rare. Here we demonstrate that two calcium-ion-dependent glycosylated enzymes, EupfF and PycR1, independently catalyse sequential, intermolecular Diels-Alder reactions in the biosynthesis of bistropolone-sesquiterpenes. We elucidate the origins of catalysis and stereoselectivity within these DAases through analysis of enzyme co-crystal structures, together with computational and mutational studies. These enzymes are secreted as glycoproteins with diverse N-glycans. The N-glycan at N211 in PycR1 significantly increases the affinity to the calcium ion, which in turn regulates the active cavity, making it specifically interact with substrates to accelerate the tandem [4 + 2] cycloaddition. The synergistic effect of the calcium ion and N-glycan on the catalytic centre of enzymes involved in secondary metabolism, especially for complex tandem reactions, can extend our understanding of protein evolution and improve the artificial design of biocatalysts.

A Single-Scan Ultraselective Heteronuclear Polarization Transfer Method for Unambiguous Complex Structure Assignment

Complex nuclear magnetic resonance (NMR) signals of organic compounds containing multiple analogous substructures or mixtures pose a significant challenge to structural identification, thus resulting in frequent misassignment of structures. The GEMSTONE method, a single-scan technique that selectively excites a specific proton signal among the crowded NMR signals, was recently proposed as a solution. However, its extension to the polarization transfer method for heteronuclear spin systems was unsuccessful. Here, we present an extension method that addresses the altered heteronuclear polarization transfer efficiency and enables the acquisition of ultraselective 13C and 1H-13C correlation NMR subspectra with hertz-level signal selectivity in both dimensions. We demonstrate the effectiveness of this technique in the structural analysis of a chromopeptide pharmaceutical and a diastereomeric mixture fungicide.

Deciphering chemical logic of fungal natural product biosynthesis through heterologous expression and genome mining

Covering: 2010 to 2022Heterologous expression of natural product biosynthetic gene clusters (BGCs) has become a widely used tool for genome mining of cryptic pathways, bottom-up investigation of biosynthetic enzymes, and engineered biosynthesis of new natural product variants. In the field of fungal natural products, heterologous expression of a complete pathway was first demonstrated in the biosynthesis of tenellin in Aspergillus oryzae in 2010. Since then, advances in genome sequencing, DNA synthesis, synthetic biology, etc. have led to mining, assignment, and characterization of many fungal BGCs using various heterologous hosts. In this review, we will highlight key examples in the last decade in integrating heterologous expression into genome mining and biosynthetic investigations. The review will cover the choice of heterologous hosts, prioritization of BGCs for structural novelty, and how shunt products from heterologous expression can reveal important insights into the chemical logic of biosynthesis. The review is not meant to be exhaustive but is rather a collection of examples from researchers in the field, including ours, that demonstrates the usefulness and pitfalls of heterologous biosynthesis in fungal natural product discovery.

Carbocycloaddition Strategies for Troponoid Synthesis

Tropone is the prototypical aromatic 7-membered ring, and can be found in virtually any undergraduate textbook as a key example of non-benzenoid aromaticity. Aside from this important historical role, tropone is also of high interest as a uniquely reactive synthon in complex chemical synthesis as well as a valuable chemotype in drug design. More recently, there has been growing interest in the utility of tropones for catalysis and material science. Thus, synthetic strategies capable of synthesizing functional tropones are key to fully exploiting the potential of this aromatic ring system. Cycloaddition reactions are particularly powerful methods for constructing carbocycles, and these strategies in turn have proven to be powerful for generating troponoids. The following review article provides an overview of strategies for troponoids wherein the 7-membered carbocycle is generated through a cycloaddition reaction. Representative examples of each strategy are also provided.

Computation-Guided Total Synthesis of Vitisinol G

Computational chemistry is useful in synthetic organic chemistry, as it can be used not only to analyze reaction mechanisms, but also to calculate biosynthetic pathways and to plan and evaluate strategies for total syntheses. Here we report the computation-guided total synthesis of vitisinol G, a resveratrol dimer.

Stereochemical and Biosynthetic Rationalisation of the Tropolone Sesquiterpenoids

This review summarises the known structures, biological activities, and biosynthetic pathways of the tropolone sesquiterpenoid family of fungal secondary metabolites. Synthesis of this knowledge allows likely structural and stereochemical misassignments to be revised and shows how the compounds can be divided into three main biosynthetic classes based on the stereochemistry of key biosynthetic steps.

Identification of the Early Steps in Herbicidin Biosynthesis Reveals an Atypical Mechanism of C-Glycosylation

Herbicidins are adenosine-derived nucleoside antibiotics with an unusual tricyclic core structure. Deletion of the genes responsible for formation of the tricyclic skeleton in Streptomyces sp. L-9-10 reveals the in vivo importance of Her4, Her5, and Her6 in the early stages of herbicidin biosynthesis. In vitro characterization of Her4 and Her5 demonstrates their involvement in an initial, two-stage C-C coupling reaction that results in net C5'-glycosylation of ADP/ATP by UDP/TDP-glucuronic acid. Biochemical analyses and intermediate trapping experiments imply a noncanonical mechanism of C-glycosylation reminiscent of NAD-dependent S-adenosylhomocysteine (SAH)-hydrolase catalysis. Structural characterization of the isolated metabolites suggests possible reactions catalyzed by Her6 and Her7. An overall herbicidin biosynthetic pathway is proposed based on these observations.

Predicting dinitrogen activation by borenium and borinium cations

The activation of thermodynamically stable and kinetically inert dinitrogen (N₂) has been a great challenge due to the significant strength of the triple bond. Recently, in an experimental study on N₂ activation by boron species, a highly reactive two-coordinated borylene broke through the limitations of traditional strategies of N₂ activation by metal species. Still, studies on metal-free N₂ activation remain underdeveloped. Here, we systematically investigate a frustrated Lewis pair (FLP) combining carbene and borenium (or borinium) cations to screen potential candidates for N₂ activation via density functional theory calculations. As a result, we found that two FLPs (closed form FLP, borenium and open form FLP, borinium) are able to activate N₂ in a thermodynamically and kinetically favorable manner, with a low energy barrier of 9.6 and 7.3 kcal mol^-1, respectively. Furthermore, aromaticity was found to play an important role in the stabilization of the products, supported by nucleus-independent chemical shift (NICS), anisotropy of the current-induced density (ACID) and electron density of delocalized bonds (EDDB) analysis. Our findings provide an alternative approach for metal-free N₂ activation, highlighting the importance of FLP chemistry and aromaticity in N₂ activation.

Harnessing ortho-Quinone Methides in Natural Product Biosynthesis and Biocatalysis

The implementation of ortho-quinone methide (o-QM) intermediates in complex molecule assembly represents a remarkably efficient strategy designed by Nature and utilized by synthetic chemists. o-QMs have been taken advantage of in biomimetic syntheses for decades, yet relatively few examples of o-QM-generating enzymes in natural product biosynthetic pathways have been reported. The biosynthetic enzymes that have been discovered thus far exhibit tremendous potential for biocatalytic applications, enabling the selective production of desirable compounds that are otherwise intractable or inherently difficult to achieve by traditional synthetic methods. Characterization of this biosynthetic machinery has the potential to shine a light on new enzymes capable of similar chemistry on diverse substrates, thus expanding our knowledge of Nature's catalytic repertoire. The presently known o-QM-generating enzymes include flavin-dependent oxidases, hetero-Diels-Alderases, S-adenosyl-l-methionine-dependent pericyclases, and α-ketoglutarate-dependent nonheme iron enzymes. In this review, we discuss their diverse enzymatic mechanisms and potential as biocatalysts in constructing natural product molecules such as cannabinoids.

Convergent biomimetic semisynthesis of disesquiterpenoid rumphellolide J

The convergent biomimetic gram-scale synthesis of disesquiterpenoid ester rumphellolide J is described. 4β,8β-Epoxycaryophyllan-5-ol was prepared in 67% yield (1.4 g) from naturally ambudant (-)-β-caryophyllene. (+)-Rumphellaoic acid A was obtained in 46% yield (2.2 g) from (-)-caryophyllene oxide. The synthesised (+)-rumphellaoic acid had an opposite specific rotation compared to that of (-)-rumphellaoic acid A isolated from nature, indicating possible occurrence of (+)-β-caryophyllene in Rumphella antipathies and Psidium guajava. Esterification of (+)-rumphellaoic acid A via acyl fluoride and alkoxide of 4β,8β-epoxycaryophyllan-5-ol gave rumphellolide J in 70% yield (1.65 g). The same structure for the synthesized product and natural isolate was proven despite the opposite specific rotation value of the intermediate acid. The short access to the terpenoids provides a material for further investigations of biological activities and valuable reference standards for the analysis of the chemical composition of various natural sources.

Total Synthesis of Gukulenin B via Sequential Tropolone Functionalizations

The synthesis of functionalized aromatic compounds is a central theme of research for modern organic chemistry. Despite the increasing finesse in the functionalization of five- and six-membered aromatic rings, their seven-membered-ring sibling, tropolone (2-hydroxy-2,4,6-cycloheptatrien-1-one), remains a challenging target for synthetic derivatization. This challenge primarily emanates from the unique structural and chemical properties of tropolonoid compounds, which often lead to unexpected and undesired reaction outcomes under conditions developed for the functionalizations of other aromatic moieties. Herein, we describe the total synthesis of one of the most complex natural tropolonoids, gukulenin B. Our synthetic route features a series of site-selective aromatic C-H bond functionalizations and C-C bond formations, whose reaction conditions are judiciously tuned to allow uncompromised performance on the tropolone nucleus. The flexibility and modularity of our synthesis are expected to facilitate further synthetic and biological studies of the gukulenin family of cytotoxins. In addition, the methods and tactics developed herein for the functionalization of the tropolone moiety could inspire and enable chemists of multiple disciplines to take advantage of this privileged yet underexplored structural motif.

Computation-guided asymmetric total syntheses of resveratrol dimers

Although computational simulation-based natural product syntheses are in their initial stages of development, this concept can potentially become an indispensable resource in the field of organic synthesis. Herein we report the asymmetric total syntheses of several resveratrol dimers based on a comprehensive computational simulation of their biosynthetic pathways. Density functional theory (DFT) calculations suggested inconsistencies in the biosynthesis of vaticahainol A and B that predicted the requirement of structural corrections of these natural products. According to the computational predictions, total syntheses were examined and the correct structures of vaticahainol A and B were confirmed. The established synthetic route was applied to the asymmetric total synthesis of (−)-malibatol A, (−)-vaticahainol B, (+)-vaticahainol A, (+)-vaticahainol C, and (−)-albiraminol B, which provided new insight into the biosynthetic pathway of resveratrol dimers. This study demonstrated that computation-guided organic synthesis can be a powerful strategy to advance the chemical research of natural products.

Although computational simulation-based natural product syntheses are in their initial stages of development, this concept can potentially become an indispensable resource in the field of organic synthesis. Here the authors report asymmetric total syntheses of several resveratrol dimers based on a comprehensive computational simulation of their biosynthetic pathways.

A Benchmark Study of Quantum Mechanics and Quantum Mechanics-Molecular Mechanics Methods for Carbocation Chemistry

Carbocations play key roles in classical organic reactions and have also been implicated in several enzyme families. A hallmark of carbocation chemistry is multitudes of competing reaction pathways, and to be able to distinguish between pathways with quantum chemical calculations, it is necessary to approach chemical accuracy for relative energies between carbocations. Here, we present an extensive study of the performance of selected density functional theory (DFT) methods in describing the thermochemistry and kinetics of carbocations and their corresponding neutral alkenes both in the gas-phase and within a hybrid quantum mechanics-molecular mechanics (QM/MM) framework. The density functionals are benchmarked against accurate ab initio methods such as CBS-QB3 and DLPNO-CCSD(T). Based on the findings in the gas-phase calculations of carbocations and alkenes, the best functionals are chosen and tested further for non-covalent interactions in model systems using QM and QM/MM methods. We compute the interaction energies between a model carbocation/alkane and model π, dipole, and hydrophobic systems using DFT and QM(DFT)/MM and compare with DLPNO-CCSD(T). These latter model systems are representative of side chains of amino acids such as phenylalanine/tyrosine, tryptophan, asparagine/glutamine, serine/threonine, methionine, and other hydrophobic groups. The Lennard-Jones parameters of the QM atoms in QM(DFT)/MM calculations are modified to obtain an optimal fit with the QM energies. Finally, a selected carbocation reaction is studied in the gas phase and in implicit chloroform solvent using QM and in explicit chloroform solvent using QM/MM and umbrella sampling simulations. This study highlights the highest accuracy possible with selected density functionals and QM/MM methods but also some limitations in using QM/MM methods for carbocation systems.

Stereochemical characterisation of the non-canonical α-humulene synthase from Acremonium strictum

The non-canonical fungal α-humulene synthase was investigated through isotopic labelling experiments for its stereochemical course regarding inversion or retention at C-1, the face selectivity at C-11, and the stereoselectivity of the final deprotonation. A new and convenient desymmetrisation strategy was developed to enable a full stereochemical analysis of the catalysed steps to the achiral α-humulene product from stereoselectively labelled farnesyl diphosphate.

Understanding and Engineering the Stereoselectivity of Humulene Synthase

The non-canonical terpene cyclase AsR6 is responsible for the formation of 2E,6E,9E-humulene during the biosynthesis of the tropolone sesquiterpenoid (TS) xenovulene A. The structures of unliganded AsR6 and of AsR6 in complex with an in crystallo cyclized reaction product and thiolodiphosphate reveal a new farnesyl diphosphate binding motif that comprises a unique binuclear Mg2+ -cluster and an essential K289 residue that is conserved in all humulene synthases involved in TS formation. Structure-based site-directed mutagenesis of AsR6 and its homologue EupR3 identify a single residue, L285/M261, that controls the production of either 2E,6E,9E- or 2Z,6E,9E-humulene. A possible mechanism for the observed stereoselectivity was investigated using different isoprenoid precursors and results demonstrate that M261 has gatekeeping control over product formation.