Publications

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Amphipod diversity and metabolomics of the Antarctic sponge Dendrilla antarctica

2022

The western Antarctic Peninsula harbours a diverse benthic marine community where dense canopies of macroalgae can dominate the shallow subtidal zone (0–40 m or greater). In the lower portion of this range (below 25–35 m depending on topography), invertebrates such as sponges and echinoderms can be found in greater abundance due to reduced competition for space from the algal species. Dendrilla antarctica (previously Dendrilla membranosa) is a common demosponge that thrives in both communities and is known for producing diterpene secondary metabolites as a defence against sympatric sea star and amphipod predators. Omnivorous mesograzers such as amphipods inhabit both communities; however, they are in greatest abundance within the macroalgal canopy. Due to the differences between habitats, it was hypothesized that specific amphipod species not susceptible to the defensive metabolites of D. antarctica would take refuge from predators in the chemically defended sponge. Analysis of the metabolome and amphipod communities from sponges in both habitats found correlations of metabolic profile to both abundance and habitat. These studies serve to inform our understanding of the complex ecosystem of the Antarctic benthos that stands to be dramatically altered by the rapidly changing climate in the years to come.

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Chemistry and Bioactivity of the Deep-Water Antarctic Octocoral Alcyonium sp.

2022

Chemical investigation of an Antarctic deep-water octocoral has led to the isolation of four new compounds, including three illudalane sesquiterpenoids (1–3) related to the alcyopterosins, a highly oxidized steroid, alcyosterone (5), and five known alcyopterosins (4, 6–9). The structures were established by extensive 1D and 2D NMR analyses, while 9 was verified by XRD. Alcyopterosins are unusual for their nitrate ester functionalization and have been characterized with cytotoxicity related to their DNA binding properties. Alcyopterosins V (3) and E (4) demonstrated single-digit micromolar activity against Clostridium difficile, an intestinal bacterium capable of causing severe diarrhea that is increasingly associated with drug resistance. Alcyosterone (5) and several alcyopterosins were similarly potent against the protist Leishmania donovani, the causative agent of leishmaniasis, a disfiguring disease that can be fatal if not treated. While the alcyopterosin family of sesquiterpenes is known for mild cytotoxicity, the observed activity against C. difficile and L. donovani is selective for the infectious agents.

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Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery

2022

The pairing of analytical chemistry with genomic techniques represents a new wave in natural product chemistry. With an increase in the availability of sequencing and assembly of microbial genomes, interrogation into the biosynthetic capability of producers with valuable secondary metabolites is possible. However, without the development of robust, accessible, and medium to high throughput tools, the bottleneck in pairing metabolic potential and compound isolation will continue. Several innovative approaches have proven useful in the nascent stages of microbial genome-informed drug discovery. Here, we consider a number of these approaches which have led to prioritization of strain targets and have mitigated rediscovery rates. Likewise, we discuss integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure. Lastly, we discuss advances in engineering, chemistry, and molecular networking and other computational approaches that are accelerating progress in the field of omic-informed natural product drug discovery. Together, these strategies enhance the synergy between cutting edge omics, chemical characterization, and computational technologies that pitch the discovery of natural products with pharmaceutical and other potential applications to the crest of the wave where progress is ripe for rapid advances.

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One Antarctic slug to confuse them all: the underestimated diversity of Doris kerguelenensis

2022

The Antarctic marine environment, although rich in life, is predicted to experience rapid and
significant effects from climate change. Despite a revolution in the approaches used to document
biodiversity, less than one percent of Antarctic marine invertebrates are represented by DNA
barcodes and we are at risk of losing biodiversity before discovery. The ease of sequencing
mitochondrial DNA barcodes has promoted this relatively ‘universal’ species identification
system across most metazoan phyla and barcode datasets are currently readily used for exploring
questions of species-level taxonomy. Here we present the most well-sampled phylogeny of the
direct-developing, Southern Ocean nudibranch mollusc, Doris kerguelenensis to date. This study
sampled over 1000 new Doris kerguelenensis specimens spanning the Southern Ocean and
sequenced the mitochondrial COI gene. Results of a maximum likelihood phylogeny and multiple
subsequent species delimitation analyses identified 27 new species in this complex (now 59 in
total). Using rarefaction techniques, we infer more species are yet to be discovered. Some
species were only collected from southern South America or the sub-Antarctic islands, while at
least four species were found spanning the Polar Front. This is contrary to dispersal predictions
for species without a larval stage such as Doris kerguelenensis. Our work demonstrates the value
of increasing geographic scope in sampling and highlights what could be lost given the current
global biodiversity crisis.

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Tongalides, Halogenated Butenolides from an Antarctic Delisea sp.
Rhodophyte

2022

Six new halogenated butenolides, tongalides A–C (1–3) and their acetylated congeners (4–6), were isolated from an extract of the Antarctic rhodophyte Delisea sp. that displayed significant antibiotic activity. The structures of the compounds were determined by analysis of data acquired by spectroscopic and spectrometric techniques including NMR, HRESIMS, optical rotation, and X-ray diffraction studies. The newly isolated compounds were assayed for antibacterial activity, but exhibited no growth inhibition of ESKAPE pathogens. The extract bioactivity was attributed to the previously reported Z-acetoxyfimbrolide A also isolated from the extract, providing further evidence that the exocyclic double bond is essential to the antibacterial activity of the structurally related fimbrolide class of metabolite.

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From Antarctica to cancer research: a novel human DNA topoisomerase 1B inhibitor from Antarctic sponge Dendrilla antarctica

2022

Nature has been always a great source of possible lead compounds to develop new drugs against several diseases. Here we report the identification of a natural compound, membranoid G, derived from the Antarctic sponge Dendrilla antarctica displaying an in vitro inhibitory activity against human DNA topoisomerase 1B. The experiments indicate that membranoid G, when pre-incubated with the enzyme, strongly and irreversibly inhibits the relaxation of supercoiled DNA. This compound completely inhibits the cleavage step of the enzyme catalytic mechanism by preventing protein binding to the DNA. Membranoid G displays also a cytotoxic effect on tumour cell lines, suggesting its use as a possible lead compound to develop new anticancer drugs.

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Australindolones, New Aminopyrimidine Substituted Indolone Alkaloids from an Antarctic Tunicate Synoicum sp.

2022

Five new alkaloids have been isolated from the lipophilic extract of the Antarctic tunicate Synoicum sp. Deep-sea specimens of Synoicum sp. were collected during a 2011 cruise of the R/V Nathanial B. Palmer to the southern Scotia Arc, Antarctica. Crude extracts from the invertebrates obtained during the cruise were screened in a zebrafish-based phenotypic assay. The Synoicum sp. extract induced embryonic dysmorphology characterized by axis truncation, leading to the isolation of aminopyrimidine substituted indolone (1–4) and indole (5–12) alkaloids. While the primary bioactivity tracked with previously reported meridianins A–G (5–11), further investigation resulted in the isolation and characterization of australindolones A–D (1–4) and the previously unreported meridianin H (12).

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Who Cares More about Chemical Defenses - the Macroalgal Producer or Its Main Grazer?

2022

The consequences of defensive secondary metabolite concentrations and interspecific metabolite diversity on grazers have been extensively investigated. Grazers which prefer certain food sources are often found in high abundance on their host and as a result, understanding the interaction between the two is important to understand community structure. The effects of intraspecific diversity, however, on the grazer are not well understood. Within a single, localized geographic area, the Antarctic red seaweed Plocamium sp. produces 15 quantitatively and qualitatively distinct mixtures of halogenated monoterpenes ("chemogroups"). Plocamium sp. is strongly chemically defended which makes it unpalatable to most grazers, except for the amphipod Paradexamine fissicauda. We investigated differences in the feeding and growth rates of both Plocamium sp. and P. fissicauda, in addition to grazer reproductive output, in relation to different chemogroups. Some chemogroups significantly reduced the grazer's feeding rate compared to other chemogroups and a non-chemically defended control. The growth rate of Plocamium sp. did not differ between chemogroups and the growth rates of P. fissicauda also did not show clear patterns between the feeding treatments. Reproductive output, however, was significantly reduced for amphipods on a diet of algae possessing one of the chemogroups when compared to a non-chemically defended control. Hence, intraspecific chemodiversity benefits the producer since certain chemogroups are consumed at a slower rate and the grazer's reproductive output is reduced. Nevertheless, the benefits outweigh the costs to the grazer as it can still feed on its host and closely associates with the alga for protection from predation.

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Gastropod assemblages associated with Himantothallus grandifolius, Sarcopeltis antarctica and other subtidal macroalgae

2022

Gastropods are an important component of subtidal Antarctic communities including in common association with macroalgae. Nonetheless, limited data exist detailing their abundance and distribution on macroalgal species. This study documents the abundance and species composition of gastropod assemblages on the two largest, blade-forming Antarctic macroalgae, Himantothallus grandifolius and Sarcopeltis antarctica, sampled across two depths (9 and 18 m) at four sites for each species off Anvers Island, Antarctica. Gastropods were also enumerated on Desmarestia anceps, Desmarestia antarctica and Plocamium sp. but were not included in the main analyses because of small sample sizes. There were major differences between the gastropod assemblages on deep vs shallow H. grandifolius and S. antarctica with much higher numbers of individuals and also greater numbers of gastropod species at the greater depth. Differences between the gastropod assemblages on H. grandifolius and S. antarctica across sampling sites were apparent in non-parametric, multivariate analyses, although depth contributed more than site to these differences. Within common sites, assemblages on H. grandifolius were significantly different from those on S. antarctica at 18 m depth but not at 9 m depth, indicating that the host species can be but is not always more important than site in influencing the gastropod assemblages.

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Tuaimenal A, a Meroterpene from the Irish Deep-Sea Soft Coral Duva florida, Displays Inhibition of the SARS-CoV-2 3CLpro Enzyme

2022

Cold water benthic environments are a prolific source of structurally diverse molecules with a range of bioactivities against human disease. Specimens of a previously chemically unexplored soft coral, Duva florida, were collected during a deep-sea cruise that sampled marine invertebrates along the Irish continental margin in 2018. Tuaimenal A (1), a cyclized merosesquiterpenoid representing a new carbon scaffold with a highly substituted chromene core, was discovered through exploration of the soft coral secondary metabolome via NMR-guided fractionation. The absolute configuration was determined through vibrational circular dichroism. Functional biochemical assays and in silico docking experiments found tuaimenal A selectively inhibits the viral main protease (3CLpro) of SARS-CoV-2.

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Not Drug-like, but Like Drugs: Cnidaria Natural Products

2022

Phylum Cnidaria has been an excellent source of natural products, with thousands of metabolites identified. Many of these have not been screened in bioassays. The aim of this study was to explore the potential of 5600 Cnidaria natural products (after excluding those known to derive from microbial symbionts), using a systematic approach based on chemical space, drug-likeness, predicted toxicity, and virtual screens. Previous drug-likeness measures: the rule-of-five, quantitative estimate of drug-likeness (QED), and relative drug likelihoods (RDL) are based on a relatively small number of molecular properties. We augmented this approach using reference drug and toxin data sets defined for 51 predicted molecular properties. Cnidaria natural products overlap with drugs and toxins in this chemical space, although a multivariate test suggests that there are some differences between the groups. In terms of the established drug-likeness measures, Cnidaria natural products have generally lower QED and RDL scores than drugs, with a higher prevalence of metabolites that exceed at least one rule-of-five threshold. An index of drug-likeness that includes predicted toxicity (ADMET-score), however, found that Cnidaria natural products were more favourable than drugs. A measure of the distance of individual Cnidaria natural products to the centre of the drug distribution in multivariate chemical space was related to RDL, ADMET-score, and the number of rule-of-five exceptions. This multivariate similarity measure was negatively correlated with the QED score for the same metabolite, suggesting that the different approaches capture different aspects of the drug-likeness of individual metabolites. The contrasting of different drug similarity measures can help summarise the range of drug potential in the Cnidaria natural product data set. The most favourable metabolites were around 210–265 Da, quite often sesquiterpenes, with a moderate degree of complexity. Virtual screening against cancer-relevant targets found wide evidence of affinities, with Glide scores <−7 in 19% of the Cnidaria natural products.

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Phenogenomic Characterization of a Newly Domesticated and Novel Species from the Genus Verrucosispora

2021

The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental gap in our knowledge of microbial diversity. Here, we present the domestication of such an organism: a previously uncultured, novel species from the rare Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic atrophy through a mixed approach of pseudogenization and reversion of pseudogenization of amino acid metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread single nucleotide polymorphism, indel, and pseudogene-impactful mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability.

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Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential

2021

The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as “Candidatus Synoicihabitans palmerolidicus.” The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium.

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Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

2021

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ∼75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression