Toward the Dark Matter of Natural Products

Considering the dynamic features of natural products, our access toward exploring the entire diversity of natural products has been quite limited. It is challenging to assess the diversity of natural products by using conventional analytical methods, even with tandem chromatographic techniques, such as LC‐MS and GC‐MS. This viewpoint is supported by the sequencing analyses of microbial genomes, which have unveiled the potential of secondary metabolite production far exceeding the number of isolated molecules. Recent advancements in metabolomics, in concert with genomics analyses, have further extended the natural product diversity, prompting growing awareness of the existence of reactive or short‐lived natural molecules. This personal account introduces some examples of the discoveries of hitherto elusive natural products, due to physico‐chemical or biological reasons, and highlights the significance of the dark matter of natural products.     

Synthesis and Evaluation of a 2,11‐Cembranoid‐Inspired Library

The 2,11‐cembranoid family of natural products has been used as inspiration for the synthesis of a structurally simplified, functionally diverse library of octahydroisobenzofuran‐based compounds designed to augment a typical medicinal chemistry library screen. Ring‐closing metathesis, lactonisation and SmI₂‐mediated methods were exemplified and applied to the installation of a third ring to mimic the nine‐membered ring of the 2,11‐cembranoids. The library was assessed for aqueous solubility and permeability, with a chemical‐space analysis performed for comparison to the family of cembranoid natural products and a sample set of a screening library. Preliminary investigations in cancer cells showed that the simpler scaffolds could recapitulate the reported anti‐migratory activity of the natural products.     

A Short Scalable Route to (−)‐α‐Kainic Acid Using Pt‐Catalyzed Direct Allylic Amination

An increased supply of scarce or inaccessible natural products is essential for the development of more sophisticated pharmaceutical agents and biological tools, and thus the development of atom‐economical, step‐economical and scalable processes to access these natural products is in high demand. Herein we report the development of a short, scalable total synthesis of (?)‐α‐kainic acid, a useful compound in neuropharmacology that is, however, limited in supply from natural resources. The synthesis features sequential platinum‐catalyzed direct allylic aminations and thermal ene‐cyclization, enabling the gram‐scale synthesis of (?)‐α‐kainic acid in six steps and 34 % overall yield.     

Total Synthesis of Camptothecin and Related Natural Products by a Flexible Strategy

A flexible strategy for constructing natural products containing indolizinone or quinolizinone scaffolds and their analogues was developed, which was based on a cascade exo hydroamination followed by spontaneous lactamization. This method was applied in the total synthesis of camptothecin in nine steps in a new ring‐forming approach. It was also used to efficiently prepare five biogenetically or structurally related natural alkaloids, including 22‐hydroxyacuminatine, oxypalmatine, norketoyobyrine, naucleficine, and nauclefine, as well as 35 natural‐product‐like molecules. We believe that this method and the small‐molecule library prepared with it can open new avenues for studying the bioactivity of camptothecin and Nauclea natural products.     

Chemoproteomic Evaluation of the Polyacetylene Callyspongynic Acid

Polyacetylenes are a class of alkyne‐containing natural products. Although potent bioactivities and thus possible applications as chemical probes have already been reported for some polyacetylenes, insights into the biological activities or molecular mode of action are still rather limited in most cases. To overcome this limitation, we describe the application of the polyacetylene callyspongynic acid in the development of an experimental roadmap for characterizing potential protein targets of alkyne‐containing natural products. To this end, we undertook the first chemical synthesis of callyspongynic acid. We then used in situ chemical proteomics methods to demonstrate extensive callyspongynic acid‐mediated chemical tagging of endoplasmic reticulum‐associated lipid‐metabolizing and modifying enzymes. We anticipate that an elucidation of protein targets of natural products may serve as an effective guide to the development of subsequent biological assays that aim to identify chemical phenotypes and bioactivities.     

Stereoselective Substrate‐Controlled Asymmetric Syntheses of both 2,5‐cis‐ and 2,5‐trans‐Tetrahydrofuranoid Oxylipids: Stereodivergent Intramolecular Amide Enolate Alkylation

The concise, highly stereoselective, substrate‐controlled asymmetric total syntheses of both 2,5‐cis‐ and 2,5‐trans‐tetrahydrofuranoid nematocidal oxylipids from the Australian brown algae Notheia anomala have been accomplished in a stereodivergent fashion. The highly stereoselective intramolecular amide enolate alkylation strategy provides access to both stereoisomers of the 3‐hydroxy‐2,5‐disubstituted tetrahydrofuran core of these marine natural products through chelate and nonchelate control, which is driven by the C3‐hydroxy protecting group. This approach offers an optional and highly stereoelective access to any of the eight possible stereoisomers of the 2,5‐disubstituted‐3‐oxygenated tetrahydrofuran skeleton, an important structural feature which is present in many biologically active natural products.     

Recent Developments in Total Syntheses of Cephalosporolides,Penisporolides, and Ascospiroketals

The possible biogenetic connection of the 10‐membered lactone (decanolide) and the tricyclic [5,5]‐spiroacetal‐cis‐fused‐γ‐lactone (SAFL) natural products was proposed by Hanson in 1985. Mimicking such biosynthetic hypothesis led us to develop a general synthetic strategy for the total syntheses of both decanolide‐type cephalosporolides and SAFL‐type natural products. This biomimetic strategy features two key transformations: i) oxidative ring expansion of bicyclic β‐hydroxy tetrahydropyrans to the decanolides and ii) ring contraction rearrangement of the decanolides to the tricyclic SAFLs. In particular, the phenol derivatives are exploited as the starting materials for the decanolides and then the SAFLs. The successful biomimetic total synthesis allows us to revise the structures and biosynthetic hypothesis of several natural products, along with development of an NMR analysis method for determination of the relative stereochemistry of SAFL‐type compounds. In addition, this account will summarize recent synthetic work by other research groups.     

Synthesis,Structural Reassignment,and Antibacterial Evaluation of 2,18‐Seco‐Lankacidinol B

Lankacidins are a group of polyketide natural products with activity against several strains of Gram‐positive bacteria. We developed a route to stereochemically diverse variants of 2,18‐seco‐lankacidinol B and found that the stereochemical assignment at C4 requires revision. This has interesting implications for the biosynthesis of natural products of the lankacidin class, all of which possessed uniform stereochemistry prior to this finding. We have evaluated 2,18‐seco‐lankacidinol B and three stereochemical derivatives against a panel of pathogenic Gram‐positive and Gram‐negative bacteria.     

Efficient Enantioselective Syntheses of Chiral Natural Products Facilitated by Ligand Design

The employment of enantioselective transition‐metal‐catalyzed transformations as key steps in asymmetric natural product syntheses have attracted considerable attention in recent years owing to their versatile synthetic utilities, mild conditions and high efficiency in chirality generation. The chiral catalysts or supporting ligands are believed to be crucial for the requisite reactivity and enantioselectivity. Therefore, the rational design of chiral ligands is at the heart of developing new asymmetric transition‐metal catalyzed reactions and provides an avenue to the asymmetric synthesis of natural products. Our group has been engaged in the development of transition‐metal‐catalyzed enantioselective cross‐coupling, cyclization and other related reactions and the application of these methodologies to natural product syntheses. In this account, we summarized our recent synthetic efforts towards the efficient total syntheses of several different types of natural products including terpenes, alkaloids and polyketides facilitated by the design of a series of versatile P‐chiral phosphorous ligands.     

Total Synthesis of Ramonanins A–D

The first total synthesis of the ramonanin family of lignan natural products is described. The short synthesis involves a 2,5‐diaryl‐3,4‐dimethylene tetrahydrofuran intermediate, which participates in an unexpectedly facile Diels–Alder dimerization, generating all four natural products. Insights into the reactivity and stereoselectivity of the key dimerization are provided through computational studies employing B3LYP/6‐31G(d) and M06‐2X/6‐31G(d) model chemistries.     

Total Synthesis of Resveratrol‐Based Natural Products Using a Palladium‐Catalyzed Decarboxylative Arylation and an Oxidative Heck Reaction

Controlled access to resveratrol‐based natural products is offered by a novel, modular concept. A common building block readily available on a large scale serves as the starting material for the introduction of structurally important aryl groups by a Pd‐catalyzed decarboxylative arylation and an oxidative Heck reaction with good yields and high stereoselectivity. The modular approach is convincingly documented by the successful synthesis of three racemic resveratrol‐based natural products (quadrangularin A, ampelopsin D, and pallidol).     

Synthesis,Structural Reassignment,and Antibacterial Evaluation of 2,18‐Seco‐Lankacidinol B

Lankacidins are a group of polyketide natural products with activity against several strains of Gram‐positive bacteria. We developed a route to stereochemically diverse variants of 2,18‐seco‐lankacidinol B and found that the stereochemical assignment at C4 requires revision. This has interesting implications for the biosynthesis of natural products of the lankacidin class, all of which possessed uniform stereochemistry prior to this finding. We have evaluated 2,18‐seco‐lankacidinol B and three stereochemical derivatives against a panel of pathogenic Gram‐positive and Gram‐negative bacteria.     

Several Enantiopure Chiral Building Blocks Derived from D‐Mannose and a Formal Synthesis of Dubiusamine C

Several multi‐functional chiral building blocks derived from D‐mannose are developed, which may find diverse utilities as sources of 1‐hydroxy‐3‐methyl structural units in enantioselective synthesis of many natural products. A formal synthesis of natural dubiusamine‐C is also presented.     

Iridium‐Catalyzed Enantioselective Synthesis of Pyrrole‐Annulated Medium‐Sized‐Ring Compounds

Enantioselective synthesis of pyrrole‐annulated medium‐sized‐ring compounds by an iridium‐catalyzed allylic dearomatization/retro‐Mannich/hydrolysis sequence is presented. Various substituted pyrrole‐annulated seven‐ and eight‐membered‐ring products were obtained under mild reaction conditions with moderate to good yields and excellent enantioselectivity. Additionally, these products contain a scaffold widely distributed in natural products and biologically active compounds. The current method provides a convenient way for accessing such pyrrole‐anuulated medium‐sized‐ring compounds.     

Collective Synthesis of Cladiellins Based on the Gold‐Catalyzed Cascade Reaction of 1,7‐Diynes

The cladiellin family of natural products, which includes molecules with various biological activities, continues to invite new synthetic studies. A gold‐catalyzed tandem reaction of 1,7‐diynes to construct the 6‐5‐bicyclic ring systems that are present in a number of natural products was developed. This reaction was applied as the key step to realize the formal and total syntheses of nine members of the cladiellin family in an enantio‐ and diastereoselective manner. This modular and efficient approach could also be used for the construction of other cladiellins, as well as their analogues, for follow‐up studies.     

Vancomycin Analogues Containing Monosaccharides Exhibit Improved Antibiotic Activity: A Combined One‐Pot Enzymatic Glycosylation and Chemical Diversification Strategy

Many natural products contain carbohydrate moieties that contribute to their biological activity. Manipulation of the carbohydrate domain of natural products through multiple glycosylations to identify new derivatives with novel biological activities has been a difficult and impractical process. We report a practical one‐pot enzymatic approach with regeneration of cosubstrates to synthesize analogues of vancomycin that contain an N‐alkyl glucosamine, which exhibited marked improvement in antibiotic activity against a vancomycin‐resistant strain of Enterococcus.     

Pentafulvene for the Synthesis of Complex Natural Products: Total Syntheses of (±)‐Pallambins A and B

The first total syntheses of pallambins A and B are enabled by the use of pentafulvene in an unprecedented Diels–Alder reaction. After elaboration of the adduct through chemoselective cyclopropanation, strategic C? H insertion affords the dense tetracyclic core of the natural products. 1,3‐Dipolar cycloaddition and palladium(II)‐catalyzed alkoxycarbonylation were leveraged for the construction of the hexacyclic scaffold en route to both natural products.     

Synthesis of Natural Atisane‐Type Diterpenoids by retro‐Biomimetic Transformations

An efficient one step, retro‐biomimetic procedure for the synthesis of natural products having the atisane structure is described (Scheme 2), natural products which are components of medicinal plants and possess relevant biological activity. Their structures were confirmed by chemical transformations and spectral data. The starting materials were the known ent‐kaur‐16‐en‐19‐oic acid ( 1 ) and ent‐trachyloban‐19‐oic acid ( 2 ), diterpenoids readily available from the waste of sunflower.     

Perquinolines A–C: Unprecedented Bacterial Tetrahydroisoquinolines Involving an Intriguing Biosynthesis

Metabolic profiling of Streptomyces sp. IB2014/016‐6 led to the identification of three new tetrahydroisoquinoline natural products, perquinolines A–C ( 1 – 3 ). Labelled precursor feeding studies and the cloning of the pqr biosynthetic gene cluster revealed that 1 – 3 are assembled by the action of several unusual enzymes. The biosynthesis starts with the condensation of succinyl‐CoA and l ‐phenylalanine catalyzed by the amino‐7‐oxononanoate synthase‐like enzyme PqrA, representing rare chemistry in natural product assembly. The second condensation and cyclization events are conducted by PqrG, an enzyme resembling an acyl‐CoA ligase. Last, ATP‐grasp RimK‐type ligase PqrI completes the biosynthesis by transferring a γ‐aminobutyric acid or β‐alanine moiety. The discovered pathway represents a new route for assembling the tetrahydroisoquinoline cores of natural products.     

Total Syntheses of (+)‐Polygalolide A and (+)‐Polygalolide B: Elucidation of the Absolute Stereochemistry and Biogenetic Implications

The total syntheses of (+)‐polygalolide A and (+)‐polygalolide B have been completed by using a carbonyl ylide cycloaddition strategy. Three of the four stereocenters, including two consecutive tetrasubstituted carbon atoms at C2 and C8, were incorporated through internal asymmetric induction from the stereocenter at C7 by a [Rh₂(OAc)₄]‐catalyzed carbonyl ylide formation/intramolecular 1,3‐dipolar cycloaddition sequence. The arylmethylidene moiety of these natural products was successfully installed by a Mukaiyama aldol‐type reaction of a silyl enol ether with a dimethyl acetal, followed by elimination under basic conditions. We have also developed an alternative approach to the carbonyl ylide precursor based on a hetero‐Michael reaction. This approach requires 18 steps, and the natural products were obtained in 9.8 and 9.3 % overall yields. Comparison of specific rotations of the synthetic materials and natural products suggests that polygalolides are biosynthesized in nearly racemic forms through a [5+2] cycloaddition between a fructose‐derived oxypyrylium zwitterion with an isoprene derivative.