Total Synthesis of Abyssomicin C and atrop-Abyssomicin C

LC-MS guided discovery of a new type of abyssomicin, glycoabyssomicin A, from a deep-sea derived Streptomyces

Glycoabyssomicin A (1), a new type of abyssomicin containing a sugar unit, was isolated from the deep-sea derived Streptomyces koyangensis SCSIO 5802 guided by LC-MS. The structure of 1 was elucidated by HR-ESI-MS, 1D-NMR (1H,13C NMR), 2D-NMR (HSQC, COSY, HMBC, NOESY), and TFA hydrolysis and acetylation reactions. In the antibacterial activities evaluation against a series of gram-positive and gram-negative bacteria, it showed inactive at the concentration of 10 μg per filter paper disc. This finding would broaden the way for discovery of more lead compounds of abyssomicins.

Progress in Lewis-Acid-Templated Diels-Alder Reactions

The synthesis of natural products with complicated architectures often requires the use of segments with functional groups that can be structurally transformed with the desired stereogenic centers. Bicyclic 𝛾-lactones have great potential as a suitable segment for natural product synthesis. However, the stereoselective construction of such functionalized bicyclic 𝛾-lactones is not as straightforward as one might expect. The template-mediated Diels-Alder reaction is one of the most powerful and versatile methods for providing bicyclic 𝛾-lactones with high regioselectivity and stereoselectivity. In this reaction, the diene is linked to the dienophile by a temporary tether, allowing the reaction to proceed efficiently, yielding a product that can be used for natural product synthesis. This review describes some important instances of the template-mediated Diels-Alder reaction and its application to the synthesis of biologically active compounds.

Bent π-Conjugation within a Macrocycle: Asymmetric Total Syntheses of Spirohexenolides A and B

Macrocycles with bent π-conjugation motif are extremely rare in nature and synthetically daunting and anticancer haouamines and spirohexenolides were representative of such rare natural products with synthetically challenging bent π-conjugation within a macrocycle. While the total synthesis of haouamines has been elegantly achieved, spirohexenolides remains an unmet synthetic challenge due to the highly strained bent 1,3,5-triene conjugation within C15 macrocycle. Inspired by the chemical synthesis of cycloparaphenylenes (CPPs) and haouamines, herein we devise a synthetic strategy to overcome the highly strained bent 1,3,5-triene conjugation within the macrocycle and achieve the first, asymmetric total synthesis of spirohexenolides A (>20 mg) and B (>50 mg). Our synthesis features strategic design of ring-closing metathesis (RCM) macrocyclization followed by double dehydration to achieve the C15 macrocycle with the deformed nonplanar 1,3,5-triene conjugation. In addition, we have developed a new enantioselective construction of highly functionalized spirotetronate fragment (northeast moiety) through RCM and Ireland-Claisen rearrangement. Our in vitro bioassay studies reveal that both spirohexenolides are cytotoxic against a panel of human cancer cells with IC50 1.2-13.3 μM and spirohexenolide A is consistently more potent (up to 3 times) than spirohexenolide B, suggesting the importance of alcohol for their bioactivity and for medicinal chemistry development.

First total synthesis of type II abyssomicins: (±)-abyssomicin 2 and (±)-neoabyssomicin B

The intramolecular Diels-Alder reaction (IMDA) of a butenolide derivative, as an entry to the type II abyssomicin scaffold, and the total synthesis of (±)-abyssomicin 2 and (±)-neoabyssomicin B are reported for the first time. A facile route to the IMDA precursor, the formation of a type I intermediate and two paths to (±)-neoabyssomicin B are also discussed.

Properties of Configurationally Stable Atropoenantiomers in Macrocyclic Natural Products and the Chrysophaentin Family

development of antibiotics, antineoplastics, and therapeutics for other diseases. Natural products are unique among all other small molecules in that they are produced by dedicated enzymatic assembly lines that are the protein products of biosynthetic gene clusters. As the products of chiral macromolecules, natural products have distinct three-dimensional shapes and stereochemistry is often encoded in their structures through the presence of stereocenters, or in the case of molecules that lack a stereocenter, the presence of an axis or plane of chirality. In the latter forms of chirality, if the barrier to rotation about the chiral axis or chiral plane is sufficiently high, stable conformers may exist allowing for isolation of discrete conformers, also known as atropisomers. Importantly, the diverse functions and biological activities of natural products are contingent upon their structures, stereochemistry and molecular shape. With continued innovation in methods for natural products discovery, synthetic chemistry, and analytical and computational tools, new insights into atropisomerism in natural products and related scaffolds are being made. As molecular complexity increases, more than one form of stereoisomerism may exist in a single compound (for example, point chirality, chiral axes, and chiral planes), sometimes creating atypical or noncanonical atropisomers, a term used to distinguish physically noninterconvertable atropisomers from typical atropisomers.Here we provide an account of the discovery and unusual structural and stereochemical features of the chrysophaentins, algal derived inhibitors of the bacterial cytoskeletal protein FtsZ and its associated protein partners. Eleven members of the chrysophaentin family have been discovered to date; seven of these are macrocyclic bis-bibenzyl ethers wherein the site of the ether linkage yields either a symmetrical or asymmetrical macrocyclic ring system. The asymmetrical ring system is highly strained and corresponds to the compounds having the most potent antimicrobial activity among the family. We review the structure elucidation and NMR properties that indicate restricted rotation between axes of two biaryl ethers, and the plane represented by the substituted 2-Z-butene bridge common to all of the macrocycles. Computational studies that corroborate high barriers to rotation about one representative plane, on the order of 20+ kcal/mol are presented. These barriers to rotation fix the conformation of the macrocycle into a bowl-like structure and suggest that an atropisomer should exist. Experimental evidence for atropisomerism is presented, consistent with computational predictions. These properties are discussed in the context of the total synthesis of 9-dechlorochrysophaenin A and its ring C isomers. Last, we discuss the implications for the presence of enantiomers in the biological activity and macrocyclization of the natural product.

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.

Abyssomicin derivatives from the rhizosphere soil actinomycete Microbispora rhizosphaerae sp. nov. TBRC6028

Three undescribed abyssomicin derivatives, including microbimisin, abyssomicins Z1, and Z2, were isolated from the soil actinomycete Microbispora rhizosphaerae sp. nov. TBRC6028. Chemical structures were determined by NMR spectroscopic data (¹H, ¹³C, COSY, HSQC, HMBC, and NOESY spectra) and the absolute configurations were verified by single-crystal X-ray diffraction analyses together with the ECD spectral data. Microbimisin and abyssomicin Z1 exhibited weak antibacterial activity against Bacillus cereus with MIC values of 25.0 and 50.0 μg/mL without cytotoxicity against MCF-7 and Vero cells at the concentration of 50 μg/mL.

Strategies for the construction of γ-spirocyclic butenolides in natural product synthesis

Over the last four decades, a number of γ-spirocyclic butenolide containing natural products, drugs, and medicinally useful synthetic compounds have been reported. In this review, we discuss diverse chemical approaches to synthesize γ-spiro butenolides and their application towards natural product synthesis. The collective perception of various methods may allow superior approaches capable of delivering efficient synthetic approaches to obtain γ-spiro butenolide comprising natural products and their hybrid analogues for further drug discovery and development.

Strategies for the synthesis of furo-pyranones and their application in the total synthesis of related natural products

The furo-pyranone framework is widely present in the molecular structure of various biologically potent natural products and un-natural small molecules, and it represents a valuable target in synthetic organic chemistry and medicinal chemistry.

Synthetic Studies on Cyclocitrinol: Construction of the ABC Ring System Based on Epoxy–Nitrile Cyclization

The stereoselective synthesis of a model compound containing the ABC ring system of cyclocitrinol was accomplished. After connecting a C ring allyltitanium segment with an A ring bi­cyclo[4.1.0]heptanone segment, the seven-membered B ring moiety was constructed by an intramolecular cyclization reaction of an epoxy nitrile. The enone moiety was introduced through an oxidative decyanation reaction, and the bicyclo[4.4.1]undecane skeleton with the highly strained olefin moiety was formed through a ring-opening reaction of the bicyclo[4.1.0]heptane substructure.

Perspectives from nearly five decades of total synthesis of natural products and their analogues for biology and medicine

Covering: 1970 to 2020By definition total synthesis is the art and science of making the molecules of living Nature in the laboratory, and by extension, their analogues. Although obvious, its application to the synthesis of molecules for biology and medicine was not always the purpose of total synthesis. In recent years, however, the field has acquired momentum as its power to reach higher molecular complexity and diversity is increasing, and as the demand for rare bioactive natural products and their analogues is expanding due to their recognised potential to facilitate biology and drug discovery and development. Today this component of total synthesis endeavors is considered highly desirable, and could be part of interdisciplinary academic and/or industrial partnerships, providing further inspiration and momentum to the field. In this review we provide a brief historical background of the emergence of the field of total synthesis as it relates to making molecules for biology and medicine. We then discuss specific examples of this practice from our laboratories as they developed over the years. The review ends with a conclusion and future perspectives for natural products chemistry and its applications to biology and medicine and other added-value contributions to science and society.

C-C Bond Cleavage Approach to Complex Terpenoids: Development of a Unified Total Synthesis of the Phomactins

The rearrangement of carbon-carbon (C-C) single bonds in readily available carbocyclic scaffolds can yield uniquely substituted carbocycles that would be challenging to construct otherwise. This is a powerful and often non-intuitive approach for complex molecule synthesis. The transition-metal-mediated cleavage of C-C bonds has the potential to broaden the scope of this type of skeletal remodeling by providing orthogonal selectivities compared to more traditional pericyclic and carbocation-based rearrangements. To highlight this emerging technology, a unified, asymmetric, total synthesis of the phomactin terpenoids was developed, enabled by the selective C-C bond cleavage of hydroxylated pinene derivatives obtained from carvone. In this full account, the challenges, solutions, and intricacies of Rh(I)-catalyzed cyclobutanol C-C cleavage in a complex molecule setting are described. In addition, details of the evolution of strategies that ultimately led to the total synthesis of phomactins A, K, P, R, and T, as well as the synthesis and structural reassignment of Sch 49027, are given.

Epoxy-Tethered Diels-Alder Reaction toward the Tricyclic Core of Kalihinols

A chiral-template-driven intramolecular Diels-Alder reaction has been used to build the tricyclic core of kalihinols, a group of antimalarial marine natural products. The key starting materials are commercially available nerol and sulcatone.

Out of the Abyss: Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins

Natural products have traditionally been discovered through the screening of culturable microbial isolates from diverse environments. The sequencing revolution allowed the identification of dozens of biosynthetic gene clusters (BGCs) within single bacterial genomes, either from cultured or uncultured strains. However, we are still far from fully exploiting the microbial reservoir, as most of the species are non-model organisms with complex regulatory systems that can be recalcitrant to engineering approaches. Genomic and metagenomic data produced by laboratories worldwide covering the range of natural and artificial environments on Earth, are an invaluable source of raw information from which natural product biosynthesis can be accessed. In the present work, we describe the environmental distribution and evolution of the abyssomicin BGC through the analysis of publicly available genomic and metagenomic data. Our results demonstrate that the selection of a pathway-specific enzyme to direct genome mining is an excellent strategy; we identified 74 new Diels–Alderase homologs and unveiled a surprising prevalence of the abyssomicin BGC within terrestrial habitats, mainly soil and plant-associated. We also identified five complete and 12 partial new abyssomicin BGCs and 23 new potential abyssomicin BGCs. Our results strongly support the potential of genome and metagenome mining as a key preliminary tool to inform bioprospecting strategies aimed at the identification of new bioactive compounds such as -but not restricted to- abyssomicins.

Biomimetic Synthesis of Psiguajdianone Guided Discovery of the Meroterpenoids from Psidium guajava

Psiguajdianone (1), a novel caryophyllene-derived meroterpenoid dimer, was isolated from Psidium guajava. The structure of 1 was determined by X-ray analysis and confirmed by total synthesis. Our synthetic strategy involves biomimetic cascade Knoevenagel condensation/hetero-Diels-Alder reaction and dimerization. Notably, the caryophyllene-derived meroterpenoids obtained during our synthesis were first identified as artifacts in the laboratory, and five of them were proven to be natural products present in the plant. Moreover, these compounds show significant anti-inflammatory activity.

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

The synthesis and antibacterial activity of two new highly truncated derivatives of the natural product abyssomicin C are reported. This work outlines the limits of structural truncation of the natural product and consequently provides insights for further structure–activity relationship studies towards novel antibiotics targeting 4-amino-4-deoxychorismate (ADC) synthase. Specifically, it is demonstrated that the synthetically challenging bicyclic motif is essential for activity towards methicillin-resistant Staphylococcus aureus (MRSA).

Marine Spirotetronates: Biosynthetic Edifices That Inspire Drug Discovery

Spirotetronates are actinomyces-derived polyketides that possess complex structures and exhibit potent and unexplored bioactivities. Due to their anticancer and antimicrobial properties, they have potential as drug hits and deserve further study. In particular, abyssomicin C and tetrocarcin A have shown significant promise against antibiotic-resistant S. aureus and tuberculosis, as well as for the treatment of various lymphomas and solid tumors. Improved synthetic routes to these compounds, particularly the class II spirotetronates, are needed to access sufficient quantities for structure optimization and clinical applications.

Total Synthesis Endeavors and Their Contributions to Science and Society:A Personal Account

The advent of organic synthesis in the 19th century, serendipitous as it was, set in motion a revolution in science that continues to evolve into increasing levels of sophistication and to expand into new domains of science and technology for the benefits of science and society. Its evolution was always driven by the challenges posed by natural products, whose structures were becoming increasingly complex and diverse. In response to these challenges, synthetic organic chemists were prompted to sharpen their art to reach their target molecules, whose structures were often confirmed only after their synthesis in the laboratory through the art and science of total synthesis. The latter became the “locomotive” and the “flagship” of organic synthesis, for through this practice novel synthetic methods were discovered and invented, and also tested for their generality, applicability, and scope with regard to molecular complexity and diversity. The purpose of total synthesis has also evolved over the years to include aspects beyond the synthesis of the molecule and confirmation of its structure. In this article, we briefly review the evolution of total synthesis in terms of its power and reach and demonstrate its current state of the art that combines fundamentals with translational aspects through examples from our laboratories. The highlighted examples reflect the newly emerged paradigm of the discipline that includes—in addition to the total synthesis of the target molecule—structural elucidations, method discovery and development, design, synthesis, and biological evaluation of analogues for biology and medicine, and training of young students, preparing them for academic and industrial careers in the various disciplines that require knowledge and skills to practice the central science of chemical synthesis. Such disciplines include chemical biology, drug discovery and development, materials science and nanotechnology, and other endeavors whose fundamentals depend and rely on the structure of the molecule and its synthesis.

Marine natural products as potential anti-tubercular agents

Tuberculosis has been one of the greatest global health challenges of all time. Although the current first-line anti-tuberculosis (anti-TB) medicines used in the clinic have reduced mortality, multidrug-resistance and extensively drug-resistance forms of the disease have now spread worldwide and become a global problem. Even so, few new clinically approved drugs have emerged during the past 30 years. Highly biodiverse marine organisms have received considerable attention for drug discovery in the past couple of decades, and emerging TB drug resistance has motivated interest in assessing marine natural products (MNPs) in the treatment of this disease. So far, more than 170 compounds have been isolated from marine organisms with anti-TB properties, ten of which exhibit potent activity and have the potential for further development. This review systematically surveys MNPs with anti-TB activity and illustrates the impact of these compounds on drug discovery research against tuberculosis.

Isolation, synthesis and bioactivity studies of phomactin terpenoids

Studies of secondary metabolites (natural products) that cover their isolation, chemical synthesis and bioactivity investigation present myriad opportunities for discovery. For example, the isolation of novel secondary metabolites can inspire advances in chemical synthesis strategies to achieve their practical preparation for biological evaluation. In the process, chemical synthesis can also provide unambiguous structural characterization of the natural products. Although the isolation, chemical synthesis and bioactivity studies of natural products are mutually beneficial, they are often conducted independently. Here, we demonstrate the benefits of a collaborative study of the phomactins, diterpenoid fungal metabolites that serve as antagonists of the platelet activating factor receptor. Our isolation of novel phomactins has spurred the development of a bioinspired, unified approach that achieves the total syntheses of six congeners. We also demonstrate in vitro the beneficial effects of several phomactins in suppressing the rate of repopulation of tumour cells following gamma radiation therapy.

Review on Abyssomicins: Inhibitors of the Chorismate Pathway and Folate Biosynthesis

Antifolates targeting folate biosynthesis within the shikimate-chorismate-folate metabolic pathway are ideal and selective antimicrobials, since higher eukaryotes lack this pathway and rely on an exogenous source of folate. Resistance to the available antifolates, inhibiting the folate pathway, underlines the need for novel antibiotic scaffolds and molecular targets. While para-aminobenzoic acid synthesis within the chorismate pathway constitutes a novel molecular target for antifolates, abyssomicins are its first known natural inhibitors. This review describes the abyssomicin family, a novel spirotetronate polyketide Class I antimicrobial. It summarizes synthetic and biological studies, structural, biosynthetic, and biological properties of the abyssomicin family members. This paper aims to explain their molecular target, mechanism of action, structure⁻activity relationship, and to explore their biological and pharmacological potential. Thirty-two natural abyssomicins and numerous synthetic analogues have been reported. The biological activity of abyssomicins includes their antimicrobial activity against Gram-positive bacteria and mycobacteria, antitumor properties, latent human immunodeficiency virus (HIV) reactivator, anti-HIV and HIV replication inducer properties. Their antimalarial properties have not been explored yet. Future analoging programs using the structure⁻activity relationship data and synthetic approaches may provide a novel abyssomicin structure that is active and devoid of cytotoxicity. Abyssomicin J and atrop-o-benzyl-desmethylabyssomicin C constitute promising candidates for such programs.

Bi- and Tetracyclic Spirotetronates from the Coal Mine Fire Isolate Streptomyces sp. LC-6-2

The structures of 12 new "enantiomeric"-like abyssomicin metabolites (abyssomicins M-X) from Streptomyces sp. LC-6-2 are reported. Of this set, the abyssomicin W (11) contains an unprecedented 8/6/6/6 tetracyclic core, while the bicyclic abyssomicin X (12) represents the first reported naturally occurring linear spirotetronate. Metabolite structures were determined based on spectroscopic data and X-ray crystallography, and Streptomyces sp. LC-6-2 genome sequencing also revealed the corresponding putative biosynthetic gene cluster.

Stereocontrolled Synthesis of Kalihinol C

We report a concise chemical synthesis of kalihinol C via a possible biosynthetic intermediate, "protokalihinol", which was targeted as a scaffold en route to antiplasmodial analogs. High stereocontrol of the kalihinol framework relies on a heterodendralene cascade to establish the target stereotetrad. Common problems of regio- and chemoselectivity encountered in the kalihinol class are explained and solved.

Rhodomentones A and B, novel meroterpenoids with unique NMR characteristics from Rhodomyrtus tomentosa

Two novel meroterpenoids were isolated from Rhodomyrtus tomentosa. Their structures with unique NMR characteristics were determined by extensive spectroscopic analysis, single-crystal X-ray diffraction, quantum molecular calculation, chemical transformation as well as total synthesis.

Spirotetronate polyketides as leads in drug discovery

The discovery of chlorothricin (1) defined a new family of microbial metabolites with potent antitumor antibiotic properties collectively referred to as spirotetronate polyketides. These microbial metabolites are structurally distinguished by the presence of a spirotetronate motif embedded within a macrocyclic core. Glycosylation at the periphery of this core contributes to the structural complexity and bioactivity of this motif. The spirotetronate family displays impressive chemical structures, potent bioactivities, and significant pharmacological potential. This review groups the family members based on structural and biosynthetic considerations and summarizes synthetic and biological studies that aim to elucidate their mode of action and explore their pharmacological potential.

Abyssomicin 2 reactivates latent HIV-1 by a PKC- and HDAC-independent mechanism

Screening of a marine natural products library afforded three new analogues of the tetronic acid containing polyketide abyssomicin family and identified abyssomicin 2 as a selective reactivator of latent HIV virus. Examination of the mode of action of this new latent HIV reactivating agent demonstrated that it functions via a distinct mechanism compared to that of existing reactivating agents and is effective at reactivating latent virus in a subset of primary patient cell lines.

A twist of nature – the significance of atropisomers in biological systems

This review encompasses the synthesis and identification of recently detected natural atropisomers with potential therapeutic activity.

Natural products with anti-Bredt and bridgehead double bonds

Well over a hundred years ago, Professor Julius Bredt embarked on a career pursuing and critiquing bridged bicyclic systems that contained ring strain induced by the presence of a bridgehead olefin. These endeavors founded what we now know as Bredt's rule (Bredtsche Regel). Physical, theoretical, and synthetic organic chemists have intensely studied this premise, pushing the boundaries of such systems to arrive at a better understood physical phenomenon. Mother nature has also seen fit to construct molecules containing bridgehead double bonds that encompass Bredt's rule. For the first time, this topic is reviewed in a natural product context.