From Complex Natural Products to Simple Synthetic Mimetics by Computational De Novo Design

We present the computational de novo design of synthetically accessible chemical entities that mimic the complex sesquiterpene natural product (?)‐Englerin A. We synthesized lead‐like probes from commercially available building blocks and profiled them for activity against a computationally predicted panel of macromolecular targets. Both the design template (?)‐Englerin A and its low‐molecular weight mimetics presented nanomolar binding affinities and antagonized the transient receptor potential calcium channel TRPM8 in a cell‐based assay, without showing target promiscuity or frequent‐hitter properties. This proof‐of‐concept study outlines an expeditious solution to obtaining natural‐product‐inspired chemical matter with desirable properties.     

Directed Hydrogenations and an Ireland–Claisen Rearrangement Linked to Evans–Tishchenko Chemistry: The Highly Efficient Total Synthesis of the Marine Cyclodepsipeptide Doliculide

Two new convergent total syntheses have been developed for the cytotoxic, actin microfilament‐stabilizing marine cyclodepsipeptide doliculide ( 1 ). A key strategic element of both routes is the establishment of the central stereogenic center of the characteristic polydeoxypropionate stereotriad by means of a hydroxyl‐directed catalytic hydrogenation of a trisubstituted double bond. The requisite olefin substrates were obtained through a modified Suzuki–Miyaura coupling or through Ireland–Claisen rearrangement of a propionate ester, respectively; the latter was the direct result of a highly selective Evans–Tishchenko reduction of a hydroxy ketone that had been obtained in a stereoselective Paterson aldol reaction. Doliculide ( 1 ) was finally obtained in a total number of 17 or 15 (14) linear steps, respectively, which represents a substantial improvement over previous syntheses of this highly bioactive natural product.     

Enantioselective Total Synthesis of (−)‐Doliculide Using Catalytic Asymmetric Hydrogenations

A concise and efficient strategy has been developed to construct a polyketide chain by employing relay asymmetric hydrogenations catalyzed by two chiral spiro iridium catalysts. By using this strategy, an enantioselective total synthesis of (?)‐doliculide has been achieved in 19 steps with 6.9 % overall yield. The route features high enantioselectivity and diastereoselectivity. The catalyst loading can be as low as 0.005 mol‐%. It is convenient to obtain natural polyketides and their analogues by this strategy.     

Aerobic Iron‐Based Cross‐Dehydrogenative Coupling Enables Efficient Diversity‐Oriented Synthesis of Coumestrol‐Based Selective Estrogen Receptor Modulators

An iron‐based cross‐dehydrogenative coupling (CDC) approach was applied for the diversity‐oriented synthesis of coumestrol‐based selective estrogen receptor modulators (SERMs), representing the first application of CDC chemistry in natural product synthesis. The first stage of the two‐step synthesis of coumestrol involved a modified aerobic oxidative cross‐coupling between ethyl 2‐(2,4‐dimethoxybenzoyl)acetate and 3‐methoxyphenol, with FeCl₃ (10 mol %) as the catalyst. The benzofuran coupling product was then subjected to sequential deprotection and lactonization steps, affording the natural product in 59 % overall yield. Based on this new methodology other coumestrol analogues were prepared, and their effects on the proliferation of the estrogen receptor (ER)‐dependent MCF‐7 and of the ER‐independent MDA‐MB‐231 breast cancer cells were tested. As a result, new types of estrogen receptor ligands having an acetamide group instead of the 9‐hydroxyl group of coumestrol were discovered. Both 9‐acetamido‐coumestrol and 8‐acetamidocoumestrol were found more active than the natural product against estrogen‐dependent MCF‐7 breast cancer cells, with IC₅₀ values of 30 and 9 nM , respectively.     

A Kinetic Self‐Sorting Approach to Heterocircuit [3]Rotaxanes

In this proof‐of‐concept study, an active‐template coupling is used to demonstrate a novel kinetic self‐sorting process. This process iteratively increases the yield of the target heterocircuit [3]rotaxane product at the expense of other threaded species.     

Natural‐Product‐Inspired Aminoepoxybenzoquinones Kill Members of the Gram‐Negative Pathogen Salmonella by Attenuating Cellular Stress Response

Gram‐negative bacteria represent a challenging task for antibacterial drug discovery owing to their impermeable cell membrane and restricted uptake of small molecules. We herein describe the synthesis of natural‐product‐derived epoxycyclohexenones and explore their antibiotic activity against several pathogenic bacteria. A compound with activity against Salmonella Typhimurium was identified, and the target enzymes were unraveled by quantitative chemical proteomics. Importantly, two protein hits were linked to bacterial stress response, and corresponding assays revealed an elevated susceptibility to reactive oxygen species upon compound treatment. The consolidated inhibition of these targets provides a rationale for antibacterial activity and highlights epoxycyclohexenones as natural product scaffolds with suitable properties for killing Gram‐negative Salmonella.     

Probing the Anticancer Mechanism of (−)‐Ainsliatrimer A through Diverted Total Synthesis and Bioorthogonal Ligation

Herein, we report an efficient approach for exploring the novel anticancer mechanism of (?)‐ainsliatrimer A, a structurally complex and unique trimeric sesquiterpenoid, through a combined strategy of diverted total synthesis (DTS) and bioorthogonal ligation (TQ ligation), which allowed us to visualize the subcellular localization of this natural product in live cells. Further biochemical studies facilitated by pretarget imaging revealed that PPARγ, a nucleus receptor, was a functional cellular target of ainsliatrimer A. We also confirmed that the anticancer activity of ainsliatrimer A was caused by the activation of PPARγ.     

A Supramolecular Stabilizer of the 14‐3‐3ζ/ERα Protein‐Protein Interaction with a Synergistic Mode of Action

We report on a stabilizer of the interaction between 14‐3‐3ζ and the Estrogen Receptor alpha (ERα). ERα is a driver in the majority of breast cancers and 14‐3‐3 proteins are negative regulators of this nuclear receptor, making the stabilization of this protein‐protein interaction (PPI) an interesting strategy. The stabilizer ( 1 ) consists of three symmetric peptidic arms containing an arginine mimetic, previously described as the GCP motif. 1 stabilizes the 14‐3‐3ζ/ERα interaction synergistically with the natural product Fusicoccin‐A and was thus hypothesized to bind to a different site. This is supported by computational analysis of 1 binding to the binary complex of 14‐3‐3 and an ERα‐derived phosphopeptide. Furthermore, 1 shows selectivity towards 14‐3‐3ζ/ERα interaction over other 14‐3‐3 client‐derived phosphomotifs. These data provide a solid support of a new binding mode for a supramolecular 14‐3‐3ζ/ERα PPI stabilizer.     

Synthesis of the Bicyclic Lactone Core of Leonuketal,Enabled by a Telescoped Diels–Alder Reaction Sequence

The Diels–Alder cycloaddition reaction has become established as a fundamental approach for the preparation of complex natural products; however, successful application of the intermolecular Diels–Alder cycloaddition reaction to the synthesis of particularly congested scaffolds remains surprisingly problematic. Inspired by the terpenoid spiroketal natural product leonuketal, a challenging telescoped reaction sequence has been realized to access the core [2.2.2]‐bicyclic lactone ring system and its [3.2.1] isomer. Our four‐step, protecting‐group‐free process required detailed investigation to circumvent the problems of adduct fragmentation and intermediate instability. Successful solution of these practical issues, along with unambiguous structural determination of the target structures, provide useful insights that will facilitate future applications of the Diels–Alder cycloaddition reaction to challenging, highly congested molecular scaffolds and ongoing synthetic efforts towards this natural product.     

Coupling Photocatalysis and Redox Biocatalysis Toward Biocatalyzed Artificial Photosynthesis

In green plants, solar‐energy utilization is accomplished through a cascade of photoinduced electron transfer, which remains a target model for realizing artificial photosynthesis. We introduce the concept of biocatalyzed artificial photosynthesis through coupling redox biocatalysis with photocatalysis to mimic natural photosynthesis based on visible‐light‐driven regeneration of enzyme cofactors. Key design principles for reaction components, such as electron donors, photosensitizers, and electron mediators, are described for artificial photosynthesis involving biocatalytic assemblies. Recent research outcomes that serve as a proof of the concept are summarized and current issues are discussed to provide a future perspective.     

Enzymatic Thioamide Formation in a Bacterial Antimetabolite Pathway

6‐Thioguanine (6TG) is a DNA‐targeting therapeutic used in the treatment of various cancers. While 6TG was rationally designed as a proof of concept for antimetabolite therapy, it is also a rare thioamide‐bearing bacterial natural product and critical virulence factor of Erwinia amylovorans, plant pathogens that cause fire blight. Through gene expression, biochemical assays, and mutational analyses, we identified a specialized bipartite enzyme system, consisting of an ATP‐dependent sulfur transferase (YcfA) and a sulfur‐mobilizing enzyme (YcfC), that is responsible for the peculiar oxygen‐by‐sulfur substitution found in the biosynthesis of 6TG. Mechanistic and phylogenetic studies revealed that YcfA‐mediated 6TG biosynthesis evolved from ancient tRNA modifications that support translational fidelity. The successful in vitro reconstitution of 6TG thioamidation showed that YcfA employs a specialized sulfur shuttle that markedly differs from universal RNA‐related systems. This study sheds light on underexplored enzymatic C?S bond formation in natural product biosynthesis.     

Scalable Biosynthesis of the Seaweed Neurochemical,Kainic Acid

Kainic acid, the flagship member of the kainoid family of natural neurochemicals, is a widely used neuropharmacological agent that helped unravel the key role of ionotropic glutamate receptors, including the kainate receptor, in the central nervous system. Worldwide shortages of this seaweed natural product in the year 2000 prompted numerous chemical syntheses, including scalable preparations with as few as six‐steps. Herein we report the discovery and characterization of the concise two‐enzyme biosynthetic pathway to kainic acid from l ‐glutamic acid and dimethylallyl pyrophosphate in red macroalgae and show that the biosynthetic genes are co‐clustered in genomes of Digenea simplex and Palmaria palmata. Moreover, we applied a key biosynthetic α‐ketoglutarate‐dependent dioxygenase enzyme in a biotransformation methodology to efficiently construct kainic acid on the gram scale. This study establishes both the feasibility of mining seaweed genomes for their biotechnological prowess.     

Scalable Biosynthesis of the Seaweed Neurochemical,Kainic Acid

Kainic acid, the flagship member of the kainoid family of natural neurochemicals, is a widely used neuropharmacological agent that helped unravel the key role of ionotropic glutamate receptors, including the kainate receptor, in the central nervous system. Worldwide shortages of this seaweed natural product in the year 2000 prompted numerous chemical syntheses, including scalable preparations with as few as six‐steps. Herein we report the discovery and characterization of the concise two‐enzyme biosynthetic pathway to kainic acid from l ‐glutamic acid and dimethylallyl pyrophosphate in red macroalgae and show that the biosynthetic genes are co‐clustered in genomes of Digenea simplex and Palmaria palmata. Moreover, we applied a key biosynthetic α‐ketoglutarate‐dependent dioxygenase enzyme in a biotransformation methodology to efficiently construct kainic acid on the gram scale. This study establishes both the feasibility of mining seaweed genomes for their biotechnological prowess.     

Targeting the Hsp90 Chaperone: Synthesis of Novel Resorcylic Acid Macrolactone Inhibitors of Hsp90

A series of benzo‐macrolactones has been prepared by chemical synthesis, and evaluated as inhibitors of heat shock protein 90 (Hsp90), an emerging attractive target for novel cancer therapeutic agents. A new synthesis of these resorcylic acid macrolactone analogues of the natural product radicicol is described in which the key steps are the acylation and ring opening of a homophthalic anhydride to give an isocoumarin, followed by a ring‐closing metathesis to form the macrocycle. The methodology has been extended to a novel series of macrolactones incorporating a 1,2,3‐triazole ring.     

Biomimetic Assembly Lines Producing Natural Product Analogs: Strategies from a Versatile Manifold to Skeletally Diverse Scaffolds

Biosynthetic assembly lines have evolved in nature, adopting divergent processes to produce a vast number of secondary metabolites. Inspired by these biogenetic processes, this account introduces recent investigations by my research group to formulate a synthetic strategy for establishing a biomimetic assembly line. With the aim not only to construct natural product‐relevant scaffolds within 5–7 steps, but also to systematically diversify skeletal and stereochemical properties and functional groups, divergent synthetic processes exploiting a versatile manifold have been developed. This approach allows for cost‐effective production of skeletally diverse and biologically active natural product analogs inaccessible by other means. Discovery of several lead candidates for a neglected tropical disease is a proof‐of‐concept of this synthetic approach.     

A Supramolecular Vesicle Based on the Complexation of p‐Sulfonatocalixarene with Protamine and its Trypsin‐Triggered Controllable‐Release Properties

Enzyme‐responsive assembly represents one of the increasingly significant topics in biomaterials research and finds feasible applications to the controlled release of therapeutic agents at specific sites at which the target enzymes are located. In this work, based on the concept of host–guest chemistry, a trypsin‐responsive supramolecular vesicle using p‐sulfonatocalix[4]arene as the macrocyclic host and natural serine protease trypsin‐cleavable cationic protein protamine as the guest molecule, is reported. The complexation of p‐sulfonatocalix[4]arene with protamine directs the formation of a supramolecular binary vesicle, which is dissipated by trypsin with high selectivity. Therefore, the present system represents a principle‐of‐concept to build a controlled‐release carrier at trypsin‐overexpressed sites.     

C−H Activation Enables a Concise Total Synthesis of Quinine and Analogues with Enhanced Antimalarial Activity

We report a novel approach to the classical natural product quinine that is based on two stereoselective key steps, namely a C?H activation and an aldol reaction, to unite the two heterocyclic moieties of the target molecule. This straightforward and flexible strategy enables a concise synthesis of natural (?)‐quinine, the first synthesis of unnatural (+)‐quinine, and also provides access to unprecedented C3‐aryl analogues, which were prepared in only six steps. We additionally demonstrate that these structural analogues exhibit improved antimalarial activity compared with (?)‐quinine both in vitro and in mice infected with Plasmodium berghei.     

Silicon‐Based Cross‐Coupling Reactions in the Total Synthesis of Natural Products

Unlike other variants of transition‐metal‐catalyzed cross‐coupling reactions, those based on organosilicon donors have not been used extensively in natural product synthesis. However, recent advances such as: 1) the development of mild reaction conditions, 2) the expansion of substrate scope, 3) the development of methods to stereoselectively and efficiently introduce the silicon‐containing moiety, 4) the development of a large number of sequential processes, and 5) the advent of bifunctional bis(silyl) linchpin reagents, signify the coming of age of silicon‐based cross‐coupling reactions. The following case studies illustrate how silicon‐based cross‐coupling reactions play a strategic role in constructing carbon–carbon bonds in selected target molecules.