Dimeric pyrrole-imidazole alkaloids: synthetic approaches and biosynthetic hypotheses

Comparative Chemical Profiling and Antimicrobial/Anticancer Evaluation of Extracts from Farmed versus Wild Agelas oroides and Sarcotragus foetidus Sponges

Marine sponges are highly efficient in removing organic pollutants and their cultivation, adjacent to fish farms, is increasingly considered as a strategy for improving seawater quality. Moreover, these invertebrates produce a plethora of bioactive metabolites, which could translate into an extra profit for the aquaculture sector. Here, we investigated the chemical profile and bioactivity of two Mediterranean species (i.e., Agelas oroides and Sarcotragus foetidus) and we assessed whether cultivated sponges differed substantially from their wild counterparts. Metabolomic analysis of crude sponge extracts revealed species-specific chemical patterns, with A. oroides and S. foetidus dominated by alkaloids and lipids, respectively. More importantly, farmed and wild explants of each species demonstrated similar chemical fingerprints, with the majority of the metabolites showing modest differences on a sponge mass-normalized basis. Furthermore, farmed sponge extracts presented similar or slightly lower antibacterial activity against methicillin-resistant Staphylococcus aureus, compared to the extracts resulting from wild sponges. Anticancer assays against human colorectal carcinoma cells (HCT-116) revealed marginally active extracts from both wild and farmed S. foetidus populations. Our study highlights that, besides mitigating organic pollution in fish aquaculture, sponge farming can serve as a valuable resource of biomolecules, with promising potential in pharmaceutical and biomedical applications.

Rapid, room-temperature self-organization of polyarylated 1H-pyrroles from acetylenes and nitriles in the KOBut/DMSO system

We have discovered that three molecules of arylacetylene are rapidly (15 min) assembled with one molecule of nitrile at room temperature in the KOBut/DMSO system to afford 2-aryl-3-arylethynyl-4-aryl-5-benzyl-1H-pyrroles in up to 76% yield. We assume that this unprecedented self-organization process involves the cascade addition of acetylenic carbanions, first to the CN, then to the CC and CC bonds of the intermediates, followed by pyrrole ring closure via the intramolecular nucleophilic addition of the NH functional group to the CC bond of the final intermediates.

Dimeric pyrrole-imidazole alkaloids: sources, structures, bioactivities and biosynthesis

Pyrrole-imidazole alkaloids (PIAs) constitute a highly diverse and densely functionalized subclass of marine natural products. Among them, the uncommon dimeric PIAs with ornate molecular architectures, attractive biological properties and interesting biosynthetic origin have spurred a considerable interest of chemists and biologists. The present review comprehensively summarized 84 dimeric PIAs discovered during the period from 1981 to September 2022, covering their source organisms, chemical structures, biological activities as well as biosynthesis. For a better understanding, these structurally intricate PIA dimers are firstly classified and presented according to their carbon skeleton features as well as biosynthesis pathways. Furthermore, relevant summaries focusing on the source organisms and the associated bioactivities of these compounds belonging to different chemical classes are also provided, which will help elucidate the fascinating chemistry and biology of these unusual PIA dimers.

Catalytic Friedel-Crafts Alkylative Desymmetrization of Cyclohexa-2,5-dienones: Access to Linear and Bridged Polycyclic Pyrroles and 3-Arylpyrroles

A catalytic [3 + 2]-cycloaddition/Friedel-Crafts alkylative desymmetrization strategy has been developed for the stereoselective construction of linear and bridged polycyclic pyrroles from alkynylcyclohexa-2,5-dienones. This strategy was further explored for the synthesis of 3-arylpyrroles under Brønsted acid catalysis. Reaction is highly chemo-, regio-, and stereoselective and is compatible with wide range of functionalized cyclohexa-2,5-dienones/pyrroles (>51 examples, ≤98% yields). Gram-scale synthesis and synthetic utility of the products have also been demonstrated to showcase the robustness of present method.

Nitrative bicyclization of 1,7-diynes for accessing skeletally diverse tricyclic pyrroles

A novel metal-free nitrative bicyclization of 1,7-diynes with ^tBuONO in the presence of H₂O is reported, producing three types of skeletally diverse tricyclic pyrroles, namely pyrrolo[3,4-c]quinolines, chromeno[3,4-c]pyrroles and benzo[e]isoindoles, with moderate to good yields by simply tuning the linkers of the 1,7-diynes. This domino protocol demonstrates remarkable compatibility regarding 1,7-diynes with different linkers, such as nitrogen and oxygen atoms and a hydroxymethyl group, and ^tBuONO plays dual roles as a nitro precursor as well as a nitrogen atom source.

Secondary metabolites from marine sponges of the genus Agelas: a comprehensive update insight on structural diversity and bioactivity

As one of the most common marine sponges in tropical and subtropical oceans, the sponges of the genus Agelas, have emerged as unique and yet under-investigated pools for discovery of natural products with fabulous molecular diversity and myriad interesting biological activities. The present review highlights the chemical structure and biological activity of 355 compounds that have been isolated and characterized from the members of Agelas sponges, over the period of about five decades (from 1971 to November 2021). For a better understanding, these numerous compounds are firstly classified and presented according to their carbon skeleton as well as their biosynthetic origins. Relevant summaries focusing on the source organism and the associated bioactivity of these compounds belonging to different chemical classes are also provided. This review highlights sponges of the genus Agelas as exciting source for discovery of intriguing natural compounds.

Efficient construction of the hexacyclic ring core of palau'amine: the pK a concept for proceeding with unfavorable equilibrium reactions

Palau'amine has received a great deal of attention as an attractive synthetic target due to its intriguing molecular architecture and significant immunosuppressive activity, and we achieved its total synthesis in 2015. However, the synthesized palau'amine has not been readily applicable to the mechanistic study of immunosuppressive activity, because it requires 45 longest linear steps from a commercially available compound. Here, we report the short-step construction of the ABCDEF hexacyclic ring core of palau'amine. The construction of the CDE tricyclic ring core in a single step is achieved by our pK_a concept for proceeding with unfavorable equilibrium reactions, and a palau'amine analog without the aminomethyl and chloride groups is synthesized in 20 longest linear steps from the same starting material. The palau'amine analog is confirmed to retain the immunosuppressive activity. The present synthetic approach for a palau'amine analog has the potential for use in the development of palau'amine probes for mechanistic elucidation.

A palau'amine analog (2) was synthesized from 2-cyclopentenone in 20 steps. The construction of the CDE tricyclic ring core in a single step is achieved by our pK_a concept for proceeding with the unfavorable equilibrium reactions.

Marine Pyrrole Alkaloids

Nitrogen heterocycles are essential parts of the chemical machinery of life and often reveal intriguing structures. They are not only widespread in terrestrial habitats but can also frequently be found as natural products in the marine environment. This review highlights the important class of marine pyrrole alkaloids, well-known for their diverse biological activities. A broad overview of the marine pyrrole alkaloids with a focus on their isolation, biological activities, chemical synthesis, and derivatization covering the decade from 2010 to 2020 is provided. With relevant structural subclasses categorized, this review shall provide a clear and timely synopsis of this area.

Pyrrole carboxamide introduction in the total synthesis of pyrrole-imidazole alkaloids

In this review various strategies for the incorporation of the signature pyrrole carboxamide moiety in the total syntheses of pyrrole-imidazole alkaloids (PIA) are discussed. These so-called oroidin alkaloids have a broad range of biological activities and display interesting skeletal diversity and complexity. These alkaloids are sponge-derived secondary metabolites and thus far more than 200 members of the PIA family have been isolated over the past few decades. Methods range from classical amide bond forming processes to non-traditional bond formation including the de novo synthesis of the pyrrole itself.

An Updated Review on the Synthesis and Antibacterial Activity of Molecular Hybrids and Conjugates Bearing Imidazole Moiety

The rapid growth of serious infections caused by antibiotic resistant bacteria, especially the nosocomial ESKAPE pathogens, has been acknowledged by Governments and scientists and is one of the world's major health problems. Various strategies have been and are currently investigated and developed to reduce and/or delay the bacterial resistance. One of these strategies regards the design and development of antimicrobial hybrids and conjugates. This unprecedented critical review, in which our continuing interest in the synthesis and evaluation of the bioactivity of imidazole derivatives is testified, aims to summarise and comment on the results obtained from the end of the 1900s until February 2020 in studies conducted by numerous international research groups on the synthesis and evaluation of the antibacterial properties of imidazole-based molecular hybrids and conjugates in which the pharmacophoric constituents of these compounds are directly covalently linked or connected through a linker or spacer. In this review, significant attention was paid to summarise the strategies used to overcome the antibiotic resistance of pathogens whose infections are difficult to treat with conventional antibiotics. However, it does not include literature data on the synthesis and evaluation of the bioactivity of hybrids and conjugates in which an imidazole moiety is fused with a carbo- or heterocyclic subunit.

Total Synthesis of (±)-Sceptrin

A four-step synthesis of the dimeric pyrrole-imidazole alkaloid sceptrin is reported. The brevity of the route is based on a simple solution developed for selective assembly of the cyclobutane core of the natural product. The photochemical intermolecular [2 + 2] dimerization of a useful hymenidin surrogate enables direct entry to this enigmatic class of biologically active marine secondary metabolites.

Precursor-Guided Mining of Marine Sponge Metabolomes Lends Insight into Biosynthesis of Pyrrole-Imidazole Alkaloids

Pyrrole-imidazole alkaloids are natural products isolated from marine sponges, holobiont metazoans that are associated with symbiotic microbiomes. Pyrrole-imidazole alkaloids have attracted attention due to their chemical complexity and their favorable pharmacological properties. However, insights into how these molecules are biosynthesized within the sponge holobionts are scarce. Here, we provide a multiomic profiling of the microbiome and metabolomic architectures of three sponge genera that are prolific producers of pyrrole-imidazole alkaloids. Using a retrobiosynthetic scheme as a guide, we mine the metabolomes of these sponges to detect intermediates in pyrrole-imidazole alkaloid biosynthesis. Our findings reveal that the nonproteinogenic amino acid homoarginine is a critical branch point that connects primary metabolite lysine to the production of pyrrole-imidazole alkaloids. These insights are derived from the polar metabolomes of these sponges which additionally reveal the presence of zwitterionic betaines that may serve important ecological roles in marine habitats. We also establish that metabolomic richness does not correlate with microbial diversity of the sponge holobiont for neither the polar nor the nonpolar metabolomes. Our findings now provide the biochemical foundation for genomic interrogation of the sponge holobiont to establish biogenetic routes for pyrrole-imidazole alkaloid production.

One-Step Synthesis of 2,5-Diaminoimidazoles and Total Synthesis of Methylglyoxal-Derived Imidazolium Crosslink (MODIC)

Here we describe a general method for the synthesis of 2,5-diaminoimidazoles, which involves a thermal reaction between α-aminoketones and substituted guanylhydrazines without the need for additives. As one of the few known ways to access the 2,5-diaminoimidazole motif, our method greatly expands the number of reported diaminoimidazoles and further supports our previous observations that these compounds spontaneously adopt the non-aromatic 4(H) tautomer. The reaction works successfully on both cyclic and acyclic amino ketone starting materials, as well as a range of substituted guanylhydrazines. Following optimization, the method was applied to the efficient synthesis of the advanced glycation end product (AGE) methylglyoxal-derived imidazolium crosslink (MODIC). We expect that this method will enable rapid access to a variety of biologically important 2,5-diaminoimidazole-containing products.

Copper-Catalyzed Cycloisomerization of Cyclopropenylimine for Synthesis of Pyrroles

Copper-catalyzed cycloisomerization of 3-iminocyclopropenes for synthesis of pyrroles has been developed. The reaction allows regioselective construction of pyrroles with various substitution patterns, including fully substituted pyrroles. The method was successfully applied to synthesis of steroidal pyrroles as well as a N-fused pyrrole.

Bromopyrrole Alkaloids from the Sponge Agelas kosrae

Two new sceptrin derivatives (1,2) and eight structurally-related known bromopyrrole-bearing alkaloids were isolated from the tropical sponge Agelas kosrae. By a combination of spectroscopic methods, the new compounds, designated dioxysceptrin (1) and ageleste C (2), were determined to be structural analogs of each other that differ at the imidazole moiety. Dioxysceptrin was also found to exist as a mixture of α-amido epimers. The sceptrin alkaloids exhibited weak cytotoxicity against cancer cells. Compounds 1 and 2 also moderately exhibited anti-angiogenic and isocitrate lyase-inhibitory activities, respectively.

Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes

Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.

A Nitrone Dipolar Cycloaddition Strategy toward an Enantioselective Synthesis of Massadine

An enantioselective route to the C,D-bicycle of massadine is reported. Enantiopure intermediates were generated by a single stereoselective reduction using the Corey-Bakshi-Shibata reagent. This initial stereoinduction was translated into the five contiguous stereocenters of the massadine D-ring by a synthetic route that features a diastereoselective and stereospecific Ireland-Claisen rearrangement of a trianionic enolate followed by a diastereoselective nitrone dipolar cycloaddition of a highly electron-poor oxime.

Rapid access to the core skeleton of the [3 + 2]-type dimeric pyrrole-imidazole alkaloids by triplet ketone-mediated C-H functionalization

The ability of triplet ketones to abstract a hydrogen atom from hydrocarbons is reminiscent of that of the high-spin metal-oxo complexes in C-H oxidation enzymes. In practice, the reactivity of triplet ketones is easier to control and applicable to promoting a wider range of reactions. We demonstrate herein the synthetic utility of triplet ketone-mediated C-addition of methanol to cyclopentenone derivatives with an expedient synthesis of the core skeleton of the [3+2]-type dimeric pyrrole-imidazole alkaloids. Remarkably, this photochemical C-H functionalization reaction is highly regioselective and can tolerate a good range of functional groups.

Isolation, Derivative Synthesis, and Structure-Activity Relationships of Antiparasitic Bromopyrrole Alkaloids from the Marine Sponge Tedania brasiliensis

The isolation and identification of a series of new pseudoceratidine (1) derivatives from the sponge Tedania brasiliensis enabled the evaluation of their antiparasitic activity against Plasmodium falciparum, Leishmania (Leishmania) amazonensis, Leishmania (Leishmania) infantum, and Trypanosoma cruzi, the causative agents of malaria, cutaneous leishmaniasis, visceral leishmaniasis, and Chagas disease, respectively. The new 3-debromopseudoceratidine (4), 20-debromopseudoceratidine (5), 4-bromopseudoceratidine (6), 19-bromopseudoceratidine (7), and 4,19-dibromopseudoceratidine (8) are reported. New tedamides A-D (9-12), with an unprecedented 4-bromo-4-methoxy-5-oxo-4,5-dihydro-1H-pyrrole-2-carboxamide moiety, are also described. Compounds 4 and 5, 6 and 7, 9 and 10, and 11 and 12 have been isolated as pairs of inseparable structural isomers differing in their sites of bromination or oxidation. Tedamides 9+10 and 11+12 were obtained as optically active pairs, indicating an enzymatic formation rather than an artifactual origin. N12-Acetylpseudoceratidine (2) and N12-formylpseudoceratidine (3) were obtained by derivatization of pseudoceratidine (1). The antiparasitic activity of pseudoceratidine (1) led us to synthesize 23 derivatives (16, 17, 20, 21, 23, 25, 27-29, 31, 33, 35, 38, 39, 42, 43, 46, 47, 50, and 51) with variations in the polyamine chain and aromatic moiety in sufficient amounts for biological evaluation in antiparasitic assays. The measured antimalarial activity of pseudoceratidine (1) and derivatives 4, 5, 16, 23, 25, 31, and 50 provided an initial SAR evaluation of these compounds as potential leads for antiparasitics against Leishmania amastigotes and against P. falciparum. The results obtained indicate that pseudoceratidine represents a promising scaffold for the development of new antimalarial drugs.

Natural products as inspiration for the development of new synthetic methods

Natural products have played an important role in shaping modern synthetic organic chemistry. In particular, their complex molecular skeletons have stimulated the development of many new synthetic methods. We highlight in this article some recent examples of synthetic design inspired by the biosynthesis of natural products.

Exploring hydroamination-cycloaddition-fragmentation sequences to access polycyclicguanidines and vinyl-2-aminoimidazoles

The intramolecular hydroamination of a guanidine on an eneyne unit affords a guanidine-substituted diene capable of reacting with dienophiles. These substrates undergo [4+2]-cycloaddition reactions to generate a series of complex cyclic- and spirocyclic-guanidines. Select substrates can further undergo a ring opening-elimination cascade that ultimately reveals a vinyl-2-aminoimidazole. As such this cascade reaction may find application in the synthesis of oroidin-type natural products and their analogues.

Muscarine, imidazole, oxazole and thiazole alkaloids

Covering: July 2012 to June 2015. Previous review: Nat. Prod. Rep., 2013, 30, 869-915The structurally diverse imidazole-, oxazole-, and thiazole-containing secondary metabolites are widely distributed in terrestrial and marine environments, and exhibit extensive pharmacological activities. In this review the latest progress involving the isolation, biological activities, and chemical and biogenetic synthesis studies on these natural products has been summarized.

Stereocontrolled Formation of a [4.4]Heterospiro Ring System with Unexpected Inversion of Configuration at the Spirocenter

Stereoselective construction of the 1,3-diazaspiro[4.4]nonane core skeleton of massadine and related dimeric pyrrole-imidazole alkaloids is a synthetic challenge. We describe herein the synthesis of all C13/14 diastereomers of this spiro molecule through controlled oxidation and epimerization of the C13 spirocenter under mild acidic conditions.

Synthesis of fused cyanopyrroles and spirocyclopropanes via addition of N-ylides to chalconimines

DABCO-ylides react as a one-carbon source with chalconimines to afford fused cyanopyrrolesvia[4 + 1] annulation and spirocyclopropanesvia[2 + 1] annulation.

Asymmetric Synthesis of Axinellamines A and B

Axinellamines A and B are broad-spectrum antibacterial pyrrole-imidazole alkaloids that have a complex polycyclic skeleton. A new asymmetric synthesis of these marine sponge metabolites is described herein, featuring an oxidative rearrangement and an anchimeric chlorination reaction.

Enantioselective β-alkylation of pyrroles with the formation of an all-carbon quaternary stereocenter

A substitutionally and configurationally inert octahedral chiral-at-metal iridium complex is reported to be an efficient catalyst for the enantioselective Friedel–Crafts alkylation of 2,5-disubstituted pyrroles at the β-position using nitroacrylates as electrophiles.

Emergence of diversity and stereochemical outcomes in the biosynthetic pathways of cyclobutane-centered marine alkaloid dimers

A deep-sea dive into the ecology and chemistry of surprising cyclobutanes from marine invertebrates.

Total synthesis of palau'amine

Palau'amine has received a great deal of attention in the past two decades as an attractive synthetic target by virtue of its intriguing molecular architecture and significant immunosuppressive activity. Here we report the total synthesis of palau'amine characterized by the construction of an ABDE tetracyclic ring core including a trans-bicylo[3.3.0]octane skeleton at a middle stage of total synthesis. The ABDE tetracyclic ring core is constructed by a cascade reaction of a cleavage of the N-N bond, including simultaneous formation of imine, the addition of amide anion to the resulting imine (D-ring formation) and the condensation of pyrrole with methyl ester (B-ring formation) in a single step. The synthetic palau'amine is confirmed to exhibit excellent immunosuppressive activity. The present synthetic route has the potential to help elucidate a pharmacophore as well as the mechanistic details of immunosuppressive activity.

Synthesis of the Carbocyclic Core of Massadine

The carbocyclic core of massadine has been synthesized relying on a stereoselective formal [3 + 2] cycloaddition of lithiumtrimethylsilyldiazomethane with α,β-unsaturated esters to form a Δ(2)-pyrazoline moiety followed by facile N-N bond cleavage. A unique feature of the current approach is the direct installation of the tertiary α-amino center and a β-cyano group in a cis arrangement on the resulting cyclopentane framework via a previously developed formal aminocyanation protocol.

Syntheses of Sceptrins and Nakamuric Acid and Insights into the Biosyntheses of Pyrrole-Imidazole Dimers

Sceptrins and nakamuric acid are structurally unique antibiotics isolated from marine sponges. Recent studies suggest that the biosynthesis of these dimeric pyrrole-imidazole alkaloids involves a single-electron transfer (SET)-promoted [2+2] cycloaddition to form their cyclobutane core skeletons. We describe herein the biomimetic syntheses of racemic sceptrin and nakamuric acid. We also report the asymmetric syntheses of sceptrin, bromosceptrin, and dibromosceptrin in their natural enantiomeric form. We further provide mechanistic insights into the pathway selectivity of the SET-promoted [2+2] and [4+2] cycloadditions that lead to the divergent formation of the sceptrin and ageliferin core skeletons. Both the [2+2] and [4+2] cycloadditions are stepwise reactions, with the [2+2] pathway kinetically and thermodynamically favored over the [4+2] pathway. For the [2+2] cycloaddition, the dimerization of pyrrole-imidazole monomers is rate-limiting, whereas for the [4+2] cycloaddition, the cyclization is the slowest step.

An approach for the synthesis of nakamuric acid

The biosynthesis of dimeric pyrrole-imidazole alkaloids is likely mediated by enzyme-catalyzed reversible single-electron transfer (SET) cycloaddition. We now show that Ir(ppy)₃ can promote SET-mediated formal [2+2] and [4+2] cycloaddition reactions of pyrrole-imidazole alkaloids-related substrates under photolytic conditions. This biomimetic approach is useful for the construction of the core skeleton of nakamuric acid and sceptrin.

Syntheses of Cyclic Guanidine-Containing Natural Products

Naturally occurring guanidine derivatives frequently display medicinally useful properties. Among them, the higher order pyrrole-imidazole alkaloids, the dragmacidins, the crambescidins/batzelladines, and the saxitoxins/tetradotoxins have stimulated the development of many new synthetic methods over the past decades. We provide here an overview of the syntheses of these cyclic guanidine-containing natural products.

Imidazoles from nitroallylic acetates and α-bromonitroalkenes with amidines: synthesis and trypanocidal activity studies

One-pot cascade reactions of amidines with nitroallylic acetates and α-bromonitroalkenes provide functionalized imidazoles that exhibit trypanocidal activity.

Synthesis of imidazoles via cascade reaction of nitroallylic acetates with amidines and studies on their trypanocidal activity

Functionalized imidazoles derived from nitroallylic acetates and amidines exhibit potent activity against T. cruzi, the etiological agent of Chagas disease.