Biogenetic space-guided synthesis of rearranged terpenoids

Natural product chemistry is constantly challenged by newly discovered, complex molecules. Elements of complexity arise from unprecedented frameworks, with a large amount of densely packed stereogenic centres and different functional groups along with a generally high oxidation state. As a prime example, rearranged triterpenoids possess all these elements. For their total synthesis, a limit of what is considered sensible in terms of steps and yield is frequently reached. As an alternative, semisynthetic approaches have gained a great amount of attention in recent years. In this featured article, we present our and others' contributions towards the development of efficient and economic syntheses of complex terpenoid natural products and elaborate on the underlying rationale of biogenetic space-guided synthetic analysis.

Puzzling Out the Structure of Novofumigatamide: Total Synthesis of Constitutional Isomers. Part II

The total synthesis of several constitutional isomers showing a different connectivity of the macrolactam ring with the hexahydropyrrolo[2,3-b]indole core, as well as those arising from the positional exchange of the valine and the anthranilate units of the structure originally proposed for (−)-novofumigatamide, has been carried out. The constitutional isomers with 12-membered ring macrolactam connected with the pyrroloindoline framework through the indole nitrogen, and the acetyl group at the pyrrole nitrogen, of endo relative configuration, were prepared through the condensation between the tryptophan and valine edges derived from l- or d-tryptophan and l-valine amino acids. The corresponding exo products are highly unstable structures difficult to isolate and characterize. A second group of isomeric structures synthesized considered the positional exchange between the valine and the anthranilate residues within the macrolactam ring in the originally proposed macrocyclic structure. Comparison of the spectroscopic data allowed us to discard these alternative structures for the natural product.

Bioinspired Synthesis of Spirochensilide A from Lanosterol

A bioinspired synthesis of spirochensilide A from commercially available lanosterol is reported. The synthesis features a directed C-H oxidation, a Wagner-Meerwein-type double methyl migration, a Meinwald rearrangement, and a double-bond isomerization/spiroketal formation cascade. The proposed biosynthetic speculation was modified by this synthetic sequence, which also served as a platform for the synthesis of other lanostanes with migrating methyl groups.

Biogenesis-Inspired, Divergent Synthesis of Spirochensilide A, Spirochensilide B, and Abifarine B Employing a Radical-Polar Crossover Rearrangement Strategy

Triterpenoids and related abeo-steroids are of interest to the scientific community for their potent and varied biological activities as well as their unique structures. Within this large and diverse family of natural products, the fir metabolites (-)-spirochensilide A and B are particularly noteworthy for their controversial biogenesis. We herein report the chemical synthesis of the spirochensilides, which involves a concerted sequence of bioinspired rearrangements contributing to its resolution. Points of divergence after each rearrangement step also allow for an approach to the abifarine family of natural products with abifarine B as a synthetic target. Key to this strategy is a radical-polar crossover event to initiate the first rearrangement without the need for a sacrificial functionality to be introduced beforehand.

Deep-Sea Natural Products from Extreme Environments: Cold Seeps and Hydrothermal Vents

The deep sea has been proven to be a great treasure for structurally unique and biologically active natural products in the last two decades. Cold seeps and hydrothermal vents, as typical representatives of deep-sea extreme environments, have attracted more and more attention. This review mainly summarizes the natural products of marine animals, marine fungi, and marine bacteria derived from deep-sea cold seeps and hydrothermal vents as well as their biological activities. In general, there were 182 compounds reported, citing 132 references and covering the literature from the first report in 1984 up to March 2022. The sources of the compounds are represented by the genera Aspergillus sp., Penicillium sp., Streptomyces sp., and so on. It is worth mentioning that 90 of the 182 compounds are new and that almost 60% of the reported structures exhibited diverse bioactivities, which became attractive targets for relevant organic synthetic and biosynthetic studies.

Bioinspired Total Synthesis of Erectones A and B, and the Revised Structure of Hyperelodione D

The field of biomimetic synthesis seeks to apply biosynthetic hypotheses to the efficient construction of complex natural products. This approach can also guide the revision of incorrectly assigned structures. Herein, we describe the evolution of a concise total synthesis and structural reassignment of hyperelodione D, a tetracyclic meroterpenoid derived from a Hypericum plant, alongside some biogenetically related natural products, erectones A and B. The key step in the synthesis of hyperelodione D forms six stereocentres and three rings in a bioinspired cascade reaction that features an intermolecular Diels-Alder reaction, an intramolecular Prins reaction and a terminating cycloetherification.

Natural product anticipation through synthesis

Natural product synthesis remains one of the most vibrant and intellectually rewarding areas of chemistry, although the justifications for pursuing it have evolved over time. In the early years, the emphasis lay on structure elucidation and confirmation through synthesis, as exemplified by celebrated studies on cocaine, morphine, strychnine and chlorophyll. This was followed by a phase where the sheer demonstration that highly complex molecules could be recreated in the laboratory in a rational manner was enough to justify the economic expense and intellectual agonies of a synthesis. Since then, syntheses of natural products have served as platforms for the demonstration of elegant strategies, for inventing new methodology 'on the fly' or to demonstrate the usefulness and scope of methods established with simpler molecules. We now add another aspect that we find fascinating, viz. 'natural product anticipation'. In this Review, we survey cases where the synthesis of a compound in the laboratory has preceded its isolation from nature. The focus of our Review lies on examples where this anticipation of a natural product has triggered a successful search or where synthesis and isolation have occurred independently. Finally, we highlight cases where a potential natural product structure has been suggested as a result of synthetic endeavours but not yet confirmed by isolation, inviting further collaborations between synthetic and natural product chemists.

Recent Achievements in Total Synthesis for Integral Structural Revisions of Marine Natural Products

A great effort to discover new therapeutic ingredients is often initiated through the discovery of the existence of novel marine natural products. Since substances produced by the marine environment might be structurally more complex and unique than terrestrial natural products, there have been cases of misassignments of their structures despite the availability of modern spectroscopic and computational chemistry techniques. When it comes to refutation to erroneously or tentatively proposed structures empirical preparations through organic chemical synthesis has the greatest contribution along with close and sophiscated inspection of spectroscopic data. Herein, we analyzed the total synthetic studies that have decisively achieved in revelation of errors, ambiguities, or incompleteness of the isolated structures of marine natural products covering the period from 2018 to 2021.

Chemoinformatic Exploration of "Bioinspired Metabolomes" Illuminates Diacetyl Assembly Pathways Toward Nesteretal A-Like Cage Molecules

An appealing and challenging cage structure along with an unusual biosynthetic pathway prompted us to explore an expeditious bioinspired one-pot total synthesis of nesteretal A. An unconventional strategy was chosen, and a cascade reaction starting from diacetyl was studied. Under organocatalytic conditions mimicking an aldolase, nesteretal A and a related cage analogue were anticipated by in silico metabolization, detected, targeted, and characterized.

Assigning the stereochemical structures of aurantinin A and B with the assistance of biosynthetic investigations

The stereochemistry of aurantinin was determined by spectroscopic and computational analysis with the assistance of biosynthetic studies. The latter method provided critical evidence for the assignment of the configuration of the 3-ketosugar moiety.

Structure Revision of Four Classes of Prenylated Aromatic Natural Products Based on a Rule for Diagnostic 13C NMR Chemical Shifts

Errors in elucidating the structures of four natural classes of prenylated aromatic compounds with 2,3-epoxy, 2,3-dihydroxy, and cyclization with an ortho-phenolic hydroxyl to give a pyran or furan ring moiety are frequent and inevitable. Based on rigorous literature research and a series of chemical transformation experiments, a rule for the rapid determination of these four classes of prenylated derivates based on ¹³C NMR data was formulated, and 57 corrections featuring these fragments were accordingly reported.

Metal-Free Synthetic Shortcut to Octahydro-Dipyrroloquinoline Skeletons from 2,5-Cyclohexadienone Derivatives and l-Proline

The tandem decarboxylative condensation-dimerization reaction of l-proline with 2,5-cyclohexadienones including p-quinone monoacetals, p-quinol ethers, and p-quinols is reported to provide a concise and rapid synthesis of octahydro-dipyrroloquinoline compounds. The reaction features the use of cost-effective and readily available starting materials, high efficiency, metal-free and green reaction conditions. The reaction is applied to the synthesis of incargranine B aglycone. The discovery of this reaction may suggest a biosynthetic pathway from 2,5-cyclohexadienones and proline for natural ingredients containing pyrroloquinoline moieties.

Biogenesis-Guided Synthesis and Structural Revision of Sarocladione Enabled by Ruthenium-Catalyzed Endoperoxide Fragmentation

Sarocladione is the first 5,10:8,9-diseco-steroid with a 14-membered macrocyclic diketone framework to have been isolated from a natural source. Herein we report a biomimetic synthesis of sarocladione in only two or seven steps from inexpensive, commercially available ergosterol. The key feature of this synthesis was a novel ruthenium-catalyzed endoperoxide fragmentation, which transformed various saturated endoperoxides into olefinic diketones by cleavage of two C-C bonds. This synthesis allowed us to unambiguously determine the structure of sarocladione and provided experimental support for its revised biosynthetic origin. This work also vividly demonstrates that consideration of the biogenesis is a powerful tool for elucidating the structures of natural products.

Minimizing the risk of deducing wrong natural product structures from NMR data

There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two-dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.

Biomimetic Total Synthesis of the Rubiginosin Meroterpenoids

Total synthesis of the Rhododendron meroterpenoids rubiginosins A and G, which both contain unusual 6-6-6-4 ring systems, has been achieved using a bioinspired cascade approach. Stepwise synthesis of these natural products, and the related 6-6-5-4 meroterpenoids fastinoid B and rhodonoid B, from naturally occurring chromene precursors is also reported.

Cyclodepsipeptide alveolaride C: total synthesis and structural assignment

First stereoselective total synthesis of naturally occurring bioactive cyclodepsipeptide alveolaride C has been achieved using a convergent approach. This synthetic study enabled us to establish unambiguously the stereochemistry of three unassigned chiral centres embedded in the nonpeptidic segment as well as revised the stereochemistry of the proposed β-phenylalanine counterpart of the molecule. The key strategic features of this synthesis include Sharpless asymmetric dihydroxylation for installing the vicinal diol moiety, Julia–Kocienski olefination for constructing the aliphatic side chain, the Shiina protocol for intermolecular esterification, amide coupling and macrolactamization for the ring formation.

First total synthesis of natural cyclodepsipeptide alveolaride C has been accomplished with an unambiguous solution to its structural riddle.

Toonasindiynes A-F, new polyacetylenes from Toona sinensis with cytotoxic and anti-inflammatory activities

The plants of genus Toona are well known for diverse limonoid secondary metabolites, while polyacetylenes are rarely found from Toona species. In this work, six new polyacetylenes toonasindiynes A-F (1-6) and six known analogues (7-12) were isolated from the root bark of Toona sinensis. Their structures and absolute configurations were elucidated by HRESIMS, 1D and 2D NMR spectroscopic analysis, modified Mosher's method, and biosynthetic consideration. These polyacetylenes share the same 4,6-diyne moiety with different side chain length and different oxidation degree. Bioactivity screening revealed the cytotoxic activity of 3, 5, 9, and 11 against U2OS cells, and the inhibitory effects on nitric oxide (NO) production of 1, 2, 5, 8, 9, and 11 in lipopolysaccharide-induced RAW 264.7 cells.

Complex Polypropionates from a South China Sea Photosynthetic Mollusk: Isolation and Biomimetic Synthesis Highlighting Novel Rearrangements

Placobranchus ocellatus is well known to produce diverse and complex γ-pyrone polypropionates. In this study, the chemical investigation of P. ocellatus from the South China Sea led to the discovery and identification of ocellatusones A-D, a series of racemic non-γ-pyrone polyketides with novel skeletons, characterized by a bicyclo[3.2.1]octane (1, 2), a bicyclo[3.3.1]nonane (3) or a mesitylene-substituted dimethylfuran-3(2H)-one core (4). Extensive spectroscopic analysis, quantum chemical computation, chemical synthesis, and/or X-ray diffraction analysis were used to determine the structure and absolute configuration of the new compounds, including each enantiomer of racemic compounds 1-4 after chiral HPLC resolution. An array of new and diversity-generating rearrangements is proposed to explain the biosynthesis of these unusual compounds based on careful structural analysis and comparison with six known co-occurring γ-pyrones (5-10). Furthermore, the successful biomimetic semisynthesis of ocellatusone A (1) confirmed the proposed rearrangement through an unprecedented acid induced cascade reaction.

Total synthesis of nafuredin B

Total synthesis of marine secondary metabolite nafuredin B has been achieved for the first time using a convergent strategy. Sharpless epoxidation followed by acid catalyzed epoxide opening were adopted to install the tetrasubstituted hydroxy center, whereas the iterative Julia-Kocienski olefination, Wittig olefination and HWE olefination afforded the olefin bonds. Ring closing metathesis in the presence of a free tetrasubstituted hydroxy group provided the unsaturated δ-lactone moiety. This synthetic study provided unambiguous structural confirmation of the isolated nafuredin B.

Orthogonal Method for Double-Bond Placement via Ozone-Induced Dissociation Mass Spectrometry (OzID-MS)

Most often, the structures of secondary metabolites are solved using a suite of NMR techniques. However, there are times when it can be challenging to position double bonds, particularly those that are fully substituted or when there are multiple double bonds in similar chemical environments. Ozone-induced dissociation mass spectrometry (OzID-MS) serves as an orthogonal structure elucidation tool, using predictable fragmentation patterns that are generated after ozonolysis across a carbon-carbon double bond. This technique is finding growing use in the lipidomics community, suggestive of its potential value for secondary metabolites. This methodology was evaluated by confirming the double-bond positions in five fungal secondary metabolites, specifically, ent-sartorypyrone E (1), sartorypyrone A (2), sorbicillin (3), trichodermic acid A (4), and AA03390 (5). This demonstrated its potential with a variety of chemotypes, ranging from polyketides to terpenoids and including those in both conjugated and nonconjugated polyenes. In addition, the potential of using this methodology in the context of a mixture was piloted by studying Aspergillus fischeri, first examining a traditional extract and then sampling a live fungal culture in situ. While the intensity of signals varied from pure compound to extract to in situ, the utility of the technique was preserved.

Recent trends in the structural revision of natural products

Covering: 2012 to 2017 This article reviews recent reports on the structural revision of natural products. Through a critical assessment of the original and revised published structures, the article addresses why each structure was targeted for revision, discusses the techniques and key discrepancies that led to the proposal of the revised structure, and offers measures that may have been taken during the original structure determination to prevent error. With the revised structures in hand, weaknesses of original proposals are assessed, providing a better understanding on the logic behind structure determination.

The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products

Computer-assisted structure elucidation can help to determine the structures of complex natural products while minimizing the risk of structure errors.

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Nature-Inspired Bioorthogonal Reaction: Development of β-Caryophyllene as a Chemical Reporter in Tetrazine Ligation

A nature-inspired bioorthogonal reaction has been developed, hinging on an inverse-electron-demand Diels-Alder reaction of tetrazine with β-caryophyllene. Readily accessible from the cheap starting material through a scalable synthesis, the newly developed β-caryophyllene chemical reporter displays appealing reaction kinetics and excellent biocompatibility, which renders it applicable to both in vitro protein labeling and live cell imaging. Moreover, it can be used orthogonally to the strain-promoted alkyne-azide cycloaddition for dual protein labeling. This work not only provides an alternative to the existing bioorthogonal reaction toolbox, but also opens a new avenue to utilize naturally occurring scaffolds as bioorthogonal chemical reporters.