Phomactin E, F, and G: new phomactin-group PAF antagonists from a marine fungus Phoma sp

Biosynthesis of Phomactin Platelet Activating Factor Antagonist Requires a Two-Enzyme Cascade

Phomactin diterpenoids possess a unique bicyclo[9.3.1]pentadecane skeleton with multiple oxidative modifications, and are good platelet-activating factor (PAF) antagonists that can inhibit PAF-induced platelet aggregation. In this study, we identified the gene cluster (phm) responsible for the biosynthesis of phomactins from a marine fungus, Phoma sp. ATCC 74077. Despite the complexity of their structures, phomactin biosynthesis only requires two enzymes: a type I diterpene cyclase PhmA and a P450 monooxygenase PhmC. PhmA was found to catalyze the formation of the phomactatriene, while PhmC sequentially catalyzes the oxidation of multiple sites, leading to the generation of structurally diverse phomactins. The rearrangement mechanism of the diterpene scaffold was investigated through isotope labeling experiments. Additionally, we obtained the crystal complex of PhmA with its substrate analogue FGGPP and elucidated the novel metal-ion-binding mode and enzymatic mechanism of PhmA through site-directed mutagenesis. This study provides the first insight into the biosynthesis of phomactins, laying the foundation for the efficient production of phomactin natural products using synthetic biology approaches.

Phomactinine, the First Nitrogen-Bearing Phomactin, Produced by Biatriospora sp. CBMAI 1333

Metabolomics analyses and improvement of growth conditions were applied toward diversification of phomactin terpenoids by the fungus Biatriospora sp. CBMAI 1333. Visualization of molecular networking results on Gephi assisted the observation of phomactin diversification and guided the isolation of new phomactin variants by applying a modified version of chemometrics based on a fractional factorial design. Consequentially, the first nitrogen-bearing phomactin, phomactinine (1), with a new rearranged carbon skeleton, was isolated and identified. The strategy combining metabolomics and chemometrics can be extended to include bioassay potency, structure novelty, and metabolic diversification connected or not to genomic analyses.

Neocucurbols A-H, Phomactin Diterpene Derivatives from the Marine-Derived Fungus Neocucurbitaria unguis-hominis FS685

Neocucurbols A-D (1-4) are diterpene derivatives that possess a complex 6/6/5/5/6 polycyclic ring system with a characteristic tetrahedrofuran bridge ring skeleton. Neocucurbols E-H (5-8) are diterpenes that feature a 6/8/6 tricyclic ring system. Their structures were unambiguously determined by detailed spectroscopic analyses, X-ray diffractions studies, and ECD calculations. All compounds (1-8) were evaluated for in vitro antimicrobial and cytotoxic activities.

Neocucurbins A-G, novel macrocyclic diterpenes and their derivatives from Neocucurbitaria unguis-hominis FS685

Three novel phomactin diterpenes neocucurbins A-C (1-3) and their derivatives, neocucurbins D-G (4-7), were isolated from the marine-derived fungus Neocucurbitaria unguis-hominis FS685. Among them, neocucurbins A-C represent the first examples of the phomactin family with an unprecedented skeleton sharing a novel polyoxygen-hetero 5/6/12 or 5/6/13 fused tricyclic ring system; whereas neocucurbins D-G feature a 5/6 fused bicyclic ring system with the opening of the macrocyclic ring, which was found in the phomactin family for the first time. Moreover, spectroscopic data analyses, single-crystal X-ray diffraction experiments, and ECD calculations were conducted to illustrate the absolute configurations of their structures. Furthermore, all seven compounds (1-7) were evaluated for their cytotoxic and antimicrobial activities.

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.

Absolute configuration of phomactatriene diterpenoids obtained by Wagner-Meerwein rearrangement of epimeric verticillols

The epimeric diterpenes (+)-(1S,3E,7E,11S,12S)-verticilla-3,7-dien-12-ol (1), isolated from Bursera suntui, and (+)-(1S,3E,7E,11S,12R)-verticilla-3,7-dien-12-ol (2), isolated from Bursera kerberi, gave the same Wagner-Meerwein rearrangement product (-)-(1E,4Z,8Z,11S,12R)-phomacta-1,(15)4,8-triene (3). The Et₂ O:BF₃ -induced transformations evidence that verticillenes and phomactanes, both containing the bicyclo[9.3.1]pentadecane skeleton, are biogenetically related through the verticillen-12-yl cation (A⁺ ), which also is a key intermediate in the biosynthetic pathways to generate antitumor taxanes. Molecular modeling using the Monte Carlo protocol, followed by density functional theory (DFT) geometry optimization employing the hybrid functionals B3LYP and B3PW91, both with the DGDZVP basis set, secured the configuration of 3 as followed from the good agreement between the calculated and experimental vibrational circular dichroism spectra. Similar DFT calculations allowed determining the absolute configuration of (+)-(1R,4R,5R,8S,9S,11S,12R,15R)-1,15:4,5:8,9-triepoxyphomactane (9), which surprisingly derives from epoxidation of the second minimum energy conformer of 3.

Marine-derived Phoma-the gold mine of bioactive compounds

The genus Phoma contains several species ubiquitously present in soil, water, and environment. There are two major groups of Phoma, viz., terrestrial and marine. After 1981 researchers all over the world have focused on marine-derived Phoma for their bioactive compounds. The marine Phoma are very rich sources for novel bioactive secondary metabolites, which could potentially be used as drugs. Recently, a large number of structurally unique metabolites with potential biological and pharmacological activities have been isolated from the marine Phoma species particularly Phoma herbarum, P. sorghina, and P. tropica. These metabolites mainly include diterpenes, enolides, lactones, quinine, phthalate, and anthraquinone. Most of these compounds possess antimicrobial, anticancer, radical scavenging, and cytotoxic properties. The present review has been focused on the general background of Phoma, current approaches used for its identification and their limitations, difference between terrestrial and marine Phoma species. In addition, this review summarizes the novel bioactive compounds derived from marine Phoma and their biological activities.

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.

Immunomodulatory Polyketides from a Phoma-like Fungus Isolated from a Soft Coral

Fourteen new polyketides with a trans-fused decalin ring system, libertalides A-N (3-16), together with two known analogues, aspermytin A and its acetate (1, 2), were isolated from the fermentation extract of a coral-derived Libertasomyces sp. fungus. Their relative configurations were elucidated on the basis of detailed spectroscopic analysis, and the absolute configurations were determined by TDDFT-ECD and optical rotation (OR) calculations. The OR of 1 and 2 were found to have opposite signs in CH₃CN and CHCl₃, which was in agreement with the OR calculations producing alternating signs for the optical rotation depending on the applied conditions. Because the signs of the OR for 1 and 2 showed high solvent dependence, they may not be used alone to correlate the absolute configurations. Compound 16 displayed structural novelty characterized by an α-enol ether bridge conjugated with an aldehyde group. In in vitro immunomodulatory screening, compounds 1, 4, and 10 significantly induced the proliferation of CD3⁺ T cells, while compounds 2, 7, 11, and 14 significantly increased the CD4⁺/CD8⁺ ratio at 3 μM. A preliminary structure-activity analysis revealed a crucial role of Δ⁷ and a terminal OH group in the regulation of CD3⁺ T cell proliferation. This is the first report of immunoregulatory activity for metabolites of this kind.

Identification of amino acid networks governing catalysis in the closed complex of class I terpene synthases

Class I terpene synthases generate the structural core of bioactive terpenoids. Deciphering structure-function relationships in the reactive closed complex and targeted engineering is hampered by highly dynamic carbocation rearrangements during catalysis. Available crystal structures, however, represent the open, catalytically inactive form or harbor nonproductive substrate analogs. Here, we present a catalytically relevant, closed conformation of taxadiene synthase (TXS), the model class I terpene synthase, which simulates the initial catalytic time point. In silico modeling of subsequent catalytic steps allowed unprecedented insights into the dynamic reaction cascades and promiscuity mechanisms of class I terpene synthases. This generally applicable methodology enables the active-site localization of carbocations and demonstrates the presence of an active-site base motif and its dominating role during catalysis. It additionally allowed in silico-designed targeted protein engineering that unlocked the path to alternate monocyclic and bicyclic synthons representing the basis of a myriad of bioactive terpenoids.

Catalytic Conia-ene and related reactions

Since its initial inception, the Conia-ene reaction, known as the intramolecular addition of enols to alkynes or alkenes, has experienced a tremendous development and appealing catalytic protocols have emerged. This review fathoms the underlying mechanistic principles rationalizing how substrate design, substrate activation, and the nature of the catalyst work hand in hand for the efficient synthesis of carbocycles and heterocycles at mild reaction conditions. Nowadays, Conia-ene reactions can be found as part of tandem reactions, and the road for asymmetric versions has already been paved. Based on their broad applicability, Conia-ene reactions have turned into a highly appreciated synthetic tool with impressive examples in natural product synthesis reported in recent years.

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.

Platelet-activating factor (PAF)-antagonists of natural origin

Presently herbal medicines are being used by about 80% of the world population for primary health care as they stood the test of time for their safety, efficacy, cultural acceptability and lesser side effects. The discovery of platelet activating factor antagonists (PAF antagonists) during these decades are going on with different framework, but the researchers led their efficiency in studying in vitro test models. Since it is assumed that PAF play a central role in etiology of many diseases in humans such as asthma, neuronal damage, migraine, cardiac diseases, inflammatory, headache etc. Present days instinctively occurring PAF antagonist exists as a specific grade of therapeutic agents for the humans against these and different diseases either laid hold of immunological or non-immunological types. Ginkgolide, cedrol and many other natural PAF antagonists such as andrographolide, α-bulnesene, cinchonine, piperine, kadsurenone, different Piper species' natural products and marine origin plants extracts or even crude drugs having PAF antagonist properties are being used currently against different inflammatory pathologies. This review is an attempt to summarize the data on PAF and action of natural PAF antagonists on it, which were evaluated by in vivo and in vitro assays.

A macrocyclic β-iodoallenolate intermediate is key: synthesis of the ABD core of phomactin A

An enantioselective strategy for the synthesis of phomactin natural products is described. The Lewis acid triggered cyclization of a β-iodoallenolate embedded in a 12-membered macrocycle was used to obtain a highly functionalized bicyclo[9.3.1]pentadecane in good yield and high diastereoselectivity. This iodoenone contains the substituents of the AD ring system of the phomactin family of natural products, appropriate for further functionalization. Synthesis of the oxadecalin core of phomactin A from the AD iodoenone intermediate was achieved. In this unusual strategy, rings A and B are both fashioned within a macrocyclic precursor.

Constructing the Architecturally Distinctive ABD-Tricycle of Phomactin A through an Intramolecular Oxa-[3 + 3] Annulation Strategy

Our efforts in constructing the ABD-ring of phomactin A through an intramolecular oxa-[3 + 3] annulation strategy is described. This struggle entailed finding a practical and efficient preparation of annulation precursor, and a realization of the unexpected competing regioisomeric pathway. The success entailed accessing the A-ring through Diels-Alder cycloaddition of Rawal's diene. Furthermore, the discovery that the regioisomers from the annulation existed as atropisomers with respect to the D-ring olefin and that they could be equilibrated to the desired ABD-tricycle, allowing large quantities of tricycle to be accessed.

Total synthesis of (±)-phomactin A. Lessons learned from respecting a challenging structural topology

Our struggles and ultimate success in achieving a total synthesis of phomactin A are described. Our strategy features an intramolecular oxa-[3 + 3] annulation to construct its unique ABD-tricyclic manifold. Although the synthesis would constitute a distinctly new approach with the 12-membered D-ring of phomactin A being assembled simultaneously with the 1-oxadecalin at an early stage, the ABD-tricycle represents a unique structural topology that would pose a number of unprecedented challenges. One challenge concerned elaborating this tricycle to have oxygenation at the proper carbon atoms. To overcome this, we would utilize a Kornblum-DeLaMare ring-opening of a peroxide bridge as well as a challenging late-stage 1,3-allylic alcohol transposition. Further, the structural intricacies of the ABD-tricycle were uncovered by a conformational analysis that would be critical for the C5a-homologation.

Terpenes from marine-derived fungi

Terpenes from marine-derived fungi show a pronounced degree of structural diversity, and due to their interesting biological and pharmacological properties many of them have aroused interest from synthetic chemists and the pharmaceutical industry alike. The aim of this paper is to give an overview of the structural diversity of terpenes from marine-derived fungi, highlighting individual examples of chemical structures and placing them in a context of other terpenes of fungal origin. Wherever possible, information regarding the biological activity is presented.

Total synthesis of phomactin A

A total synthesis of (+/-)-phomactin A is described to highlight the final completion of a complex natural product target that had commenced with an intramolecular oxa-[3 + 3] annulation strategy in the construction of the ABD-tricycle. These efforts reveal structural intricacies of this ABD-tricycle with an illustrative example being the conformational analysis that was ultimately critical for the C5a-homolgation.

An Enantioselective Synthesis of the ABD Tricycle for (-)-Phomactin A Featuring Rawal's Asymmetric Diels-Alder Cycloaddition

An enantioselective synthesis of the ABD-ring of (-)-phomactin A is described here. The sequence features Rawal's asymmetric Diels-Alder cycloaddition. The overall length is significantly reduced from our previous attempt.

Intramolecular cyclohexadienone annulations of Fischer carbene complexes: model studies for the synthesis of Phomactins

The intramolecular cyclohexadienone annulation of chromium carbene complexes is examined as a method to provide general access to the Phomactin family of natural products. The importance of the stereochemistry of the carbene complex and the number of carbons in the tether connecting the carbene complex and the alkyne are probed. Additionally, the degree of the 1,4-asymmetric induction is examined.

Studies toward the synthesis of phomactin A. An approach to the macrocyclic core

An approach to the macrocyclic core of phomactin A is described. Central to this strategy is the use of a cis-fused oxadecalin intermediate, prepared using the dihydropyrone Diels-Alder reaction. The conformational bias inherent to this system is then used to facilitate macrocycle formation via an intramolecular B-alkyl Suzuki coupling.

Regioselective Pd-Catalyzed Synthesis and Application of 3-Methyl-5-bromo-2-pyrone toward Keto-phomactin A

[Structure: see text] An efficient one-step synthetic protocol for 3-methyl-5-bromo-2-pyrone was developed using the C3-selective Pd-catalyzed coupling reaction of 3,5-dibromo-2-pyrone with Me3Al-dimethylaminoethanol complex. A subsequent seven-step reaction sequence provided a cyclohexenyl bromide, which served as the key intermediate for the synthesis of the keto analogue of phomactin A, in 31% overall yield.

The phomactins. A novel group of terpenoid platelet activating factor antagonists related biogenetically to the taxanes

A description of the structurally unusual "phomactin" family of platelet activating factor antagonists recently found in the marine fungus Phoma sp. is presented. The phomactins show an interesting structural and biosynthetic relationship with the more familiar taxane group of antitumor compounds isolated from yew trees. The Account highlights and discusses this unique relationship and also presents a cogent picture of plausible biogenetic interrelationships within the family of phomactins. Complementary synthetic endeavors with the phomactins are interwoven in the discussions, alongside contemporaneous biosynthetic studies with both the phomactins and the taxanes.

Marine natural products

This review covers the literature published in 2004 for marine natural products, with 693 citations (491 for the period January to December 2004) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, coelenterates, bryozoans, molluscs, tunicates and echinoderms. The emphasis is on new compounds (716 for 2004), together with their relevant biological activities, source organisms and country of origin. Biosynthetic studies (8), and syntheses (80), including those that lead to the revision of structures or stereochemistries, have been included.

Bioprocess Engineering Data on the Cultivation of Marine Prokaryotes and Fungi

The temperature/pressure dependency of marine prokaryotes and fungi, in terms of their growth behaviour as well as their potential to produce new metabolites or enzymes, is evaluated. Advanced shake-flask cultivations and controlled bioreactor cultivations following the batch-type, fed-batch-type and/or continuous-type procedures are summarized. After a summary of the fermentation data available so far, values on maximal biomass, specific growth rates, and (sub)optimal production yields are presented. The application of mesophilic microbes, especially bioactive metabolites, to intensify bioprocess engineering studies, is the goal. Cold-active enzymes and thermostable enzymes are the targets of experiments with psychrophilic and hyperthermophilic enzymes. A special challenge to bioengineers is also provided by barophilic strains originating from depths of, say, nearly 11000 m, or from hydrothermal vents.

Novel phomactin analogues as PAF receptor ligands

A range of natural and unnatural phomactins, recently synthesised in our laboratory, were found to exhibit PAF antagonism with pIC(50) values in the range 5.6-6.2. The variation in structural and stereochemical features between the phomactins was found to have only a modest effect on the inhibition of binding of PAF to its human platelet receptors.

Proposed mechanism for diterpene synthases in the formation of phomactatriene and taxadiene

To obtain insight into how the cyclization pathway is controlled, the mechanism of diterpene synthase reactions (the putative phomactatriene synthase and taxadiene synthases) involving the same intermediate was investigated in detail. The mechanism of the initial transformation of GGDP to verticillen-12-yl cation (A+) was proposed based on the labelling pattern of phomactatriene (9a) obtained in the feeding experiments with 13C-labelled acetates. To obtain information on the reaction pathway of A+ to 9a and taxadiene, reactions of verticillol with various acids were conducted. Structural determination of products allowed us to propose a reaction pathway via cations A+, D+, E+, F+ and G+. Identification of hydrocarbons in mycelial extracts of phomactin-producing fungus supported the proposed reaction mechanism. Based on the results of ab initio calculations for highly flexible cation intermediates, a mechanism is proposed.

Unique structural topology and reactivities of the ABD tricycle in phomactin A

Stereoselective and transannular reactivities are described for the ABD tricyclic manifold of phomactin A that possesses a unique structural topology.