Export 354 results:
Sort by: Author Title Type [ Year  (Desc)]
Almaliti, J, Miller B, Pietraszkiewicz H, Glukhov E, Naman CB, Kline T, Hanson J, Li XF, Zhou SH, Valeriote FA, Gerwick WH.  2019.  Exploration of the carmaphycins as payloads in antibody drug conjugate anticancer agents. European Journal of Medicinal Chemistry. 161:416-432.   10.1016/j.ejmech.2018.10.024   AbstractWebsite

Antibody-drug conjugates (ADCs) represent a new dimension of anticancer chemotherapeutics, with warheads to date generally involving either antitubulin or DNA-directed agents to achieve low-to sub-nanomolar potency. However, other potent cytotoxins working by different pharmacological mechanisms are under investigation, such as alpha,beta-epoxyketone based proteasome inhibitors. These proteasome active agents are an emerging class of anticancer drug that possesses ultra-potent cytotoxicity to some cancer cell lines. The carmaphycins are representatives of this latter class that we isolated and characterized from a marine cyanobacterium, and these as well as several synthetic analogues exhibit this level of potency. In the current work, we investigated the use of these highly potent cytotoxic compounds as warheads in the design of novel ADCs. We designed and synthesized a library of carmaphycin B analogues that contain amine handles, enabling their attachment to an antibody linker. The basicity of these incorporated amine handles was shown to strongly affect their cytotoxic properties. Linear amines resulted in the greatest reduction in cytotoxicity whereas less basic aromatic amines retained potent activity as demonstrated by a 4-sulfonylaniline derivative. These investigations resulted in identifying the P2 residue in the carmaphycins as the most suitable site for linker attachment point, and hence, we synthesized a highly potent analogue of carmaphycin B that contained a 4-sulfonylaniline handle as an attachment point for the linker antibody. (C) 2018 Elsevier Masson SAS. All rights reserved.

Via, CW, Glukhov E, Costa S, Zimba PV, Moeller PDR, Gerwick WH, Bertin MJ.  2018.  The metabolome of a cyanobacterial bloom visualized by MS/MS-based molecular networking reveals new neurotoxic smenamide analogs (C, D, and E). Frontiers in Chemistry. 6   10.3389/fchem.2018.00316   AbstractWebsite

Members of the cyanobacterial genus Trichodesmium are well known for their substantial impact on nitrogen influx in ocean ecosystems and the enormous surface blooms they form in tropical and subtropical locations. However, the secondary metabolite composition of these complex environmental bloom events is not well known, nor the possibility of the production of potent toxins that have been observed in other bloom-forming marine and freshwater cyanobacteria species. In the present work, we aimed to characterize the metabolome of a Trichodesmium bloom utilizing MS/MS-based molecular networking. Furthermore, we integrated cytotoxicity assays in order to identify and ultimately isolate potential cyanotoxins from the bloom. These efforts led to the isolation and identification of several members of the smenamide family, including three new smenamide analogs (1-3) as well as the previously reported smenothiazole A-hybrid polyketide-peptide compounds. Two of these new smenamides possessed cytotoxicity to neuro-2A cells (1 and 3) and their presence elicits further questions as to their potential ecological roles. HPLC profiling and molecular networking of chromatography fractions from the bloom revealed an elaborate secondary metabolome, generating hypotheses with respect to the environmental role of these metabolites and the consistency of this chemical composition across genera, space and time.

Huang, QL, Chen J, Zhang WJ, Zhou BP, Zhang CL, Gerwick WH, Cao ZY.  2018.  Alkaloids from Corydalis decumbens suppress neuronal excitability in primary cultures of mouse neocortical neurons. Phytochemistry. 150:85-92.   10.1016/j.phytochem.2018.03.006   AbstractWebsite

Eight previously undescribed alkaloids, named corydemine, dihydrocorydemine, corydedine, 8,13-dioxo-14-hydroxytetrahydropalmatine, egenine-alpha-N-oxide, egenine-beta-N-oxide, 7'-O-ethylegenine-alpha-N-oxide, and 7'-O-ethylegenine-beta-N-oxide, together with three known ones, muramine, L-tetrahydropalmatine, and (+)-egenine, were isolated from the bulbs of Corydalis decumbens. Their structures were elucidated by comprehensive spectroscopic analysis and chemical correlation. The isolated compounds were tested for their ability to modulate neuronal excitability in primary cultured neocortical neurons. Four of the compounds, corydemine, dihydrocorydemine, muramine, and L-tetrahydropalmatine, inhibited neuronal excitability with IC50 values of 3.6, 16.7, 13.5 and 14.0 mu M, respectively. (C) 2018 Elsevier Ltd. All rights reserved.

Skiba, MA, Sikkema AP, Moss NA, Lowell AN, Su M, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL.  2018.  Biosynthesis of t-Butyl in apratoxin A: functional analysis and architecture of a PKS loading module. Acs Chemical Biology. 13:1640-1650.   10.1021/acschembio.8b00252   AbstractWebsite

The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here, we determine that the apratoxin A t-butyl group is formed as a pivaloyl acyl carrier protein (ACP) by AprA, the polyketide synthase (PKS) loading module of the apratoxin A biosynthetic pathway. AprA contains an inactive "pseudo" GCN5-related N-acetyltransferase domain (Psi GNAT) flanked by two methyltransferase domains (MT1 and MT2) that differ distinctly in sequence. Structural, biochemical, and precursor incorporation studies reveal that MT2 catalyzes unusually coupled decarboxylation and methylation reactions to transform dimethylmalonyl-ACP, the product of MT1, to pivaloyl-ACP. Further, pivaloyl-ACP synthesis is primed by the fatty acid synthase malonyl acyltransferase (FabD), which compensates for the Psi GNAT and provides the initial aryl-transfer step to form AprA malonyl-ACP. Additionally, images of AprA from negative stain electron microscopy reveal multiple conformations that may facilitate the individual catalytic steps of the multienzyme module.

Wang, JL, Zheng JC, Huang CH, Zhao JY, Lin JJ, Zhou XZ, Naman CB, Wang N, Gerwick WH, Wang QW, Yan XJ, Cui W, He S.  2018.  Eckmaxol, a phlorotannin extracted from ecklonia maxima, produces anti-ss-amyloid oligomer neuroprotective effects possibly via directly acting on glycogen synthase kinase 3 ss. Acs Chemical Neuroscience. 9:1349-1356.   10.1021/acschemneuro.7b00527   AbstractWebsite

Alzheimer's disease is a progressive neurodegenerative disorder that mainly affects the elderly. Soluble ss-amyloid oligomer, which can induce neurotoxicity, is generally regarded as the main neurotoxin in Alzheimer's disease. Here we report that eckmaxol, a phlorotannin extracted from the brown alga Ecklonia maxima, could produce neuroprotective effects in SH-SY5Y cells. Eckmaxol effectively prevented but did not rescue ss-amyloid oligomer-induced neuronal apoptosis and increase of intracellular reactive oxygen species. Eckmaxol also significantly reversed the decreased expression of phospho-Ser9-glycogen synthase kinase 3 ss and increased expression of phospho-extracellular signal-regulated kinase, which was induced by A ss oligomer. Moreover, both glycogen synthase kinase 3 ss and mitogen activated protein kinase inhibitors produced neuroprotective effects in SH-SY5Y cells. Furthermore, eckmaxol showed favorable interaction in the ATP binding site of glycogen synthase kinase 3 ss and mitogen activated protein kinase. These results suggested that eckmaxol might produce neuroprotective effects via concurrent inhibition of glycogen synthase kinase 3 ss and extracellular signal-regulated kinase pathways, possibly via directly acting on glycogen synthase kinase 3 ss and mitogen activated protein kinase. Based on the central role that ss-amyloid oligomers play in the pathogenesis of Alzheimer's disease and the high annual production of Ecklonia maxima for alginate and other nutritional ingredients, this report represents a new candidate for the treatment of Alzheimer's disease, and also expands the potential application of Ecklonia maxima and its constituents in the field of pharmacology.

O'Rourke, A, Kremb S, Duggan BM, Sioud S, Kharbatia N, Raji M, Emwas AH, Gerwick WH, Voolstra CR.  2018.  Identification of a 3-Alkylpyridinium Compound from the Red Sea Sponge Amphimedon chloros with In Vitro Inhibitory Activity against the West Nile Virus NS3 Protease. Molecules. 23   10.3390/molecules23061472   AbstractWebsite

Viruses are underrepresented as targets in pharmacological screening efforts, given the difficulties of devising suitable cell-based and biochemical assays. In this study we found that a pre-fractionated organic extract of the Red Sea sponge Amphimedon chloros was able to inhibit the West Nile Virus NS3 protease (WNV NS3). Using liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy, the identity of the bioactive compound was determined as a 3-alkylpyridinium with m/z = 190.16. Diffusion Ordered Spectroscopy (DOSY) NMR and NMR relaxation rate analysis suggest that the bioactive compound forms oligomers of up to 35 kDa. We observed that at 9.4 mu g/mL there was up to 40-70% inhibitory activity on WNV NS3 protease in orthogonal biochemical assays for solid phase extracts (SPE) of A. chloros. However, the LC-MS purified fragment was effective at inhibiting the protease up to 95% at an approximate amount of 2 mu g/mL with negligible cytotoxicity to HeLa cells based on a High-Content Screening (HCS) cytological profiling strategy. To date, 3-alkylpyridinium type natural products have not been reported to show antiviral activity since the first characterization of halitoxin, or 3-alkylpyridinium, in 1978. This study provides the first account of a 3-alkylpyridinium complex that exhibits a proposed antiviral activity by inhibiting the NS3 protease. We suggest that the here-described compound can be further modified to increase its stability and tested in a cell-based assay to explore its full potential as a potential novel antiviral capable of inhibiting WNV replication.

Kristoffersen, V, Rama T, Isaksson J, Andersen JH, Gerwick WH, Hansen E.  2018.  Characterization of rhamnolipids produced by an Arctic marine bacterium from the Pseudomonas fluorescence group. Marine Drugs. 16   10.3390/md16050163   AbstractWebsite

The marine environment is a rich source of biodiversity, including microorganisms that have proven to be prolific producers of bioactive secondary metabolites. Arctic seas are less explored than warmer, more accessible areas, providing a promising starting point to search for novel bioactive compounds. In the present work, an Arctic marine Pseudomonas sp. belonging to the Pseudomonas (P.) fluorescence group was cultivated in four different media in an attempt to activate biosynthetic pathways leading to the production of antibacterial and anticancer compounds. Culture extracts were pre-fractionated and screened for antibacterial and anticancer activities. One fraction from three of the four growth conditions showed inhibitory activity towards bacteria and cancer cells. The active fractions were dereplicated using molecular networking based on MS/MS fragmentation data, indicating the presence of a cluster of related rhamnolipids. Six compounds were isolated using HPLC and mass-guided fractionation, and by interpreting data from NMR and high-resolution MS/MS analysis; the structures of the compounds were determined to be five mono-rhamnolipids and the lipid moiety of one of the rhamnolipids. Molecular networking proved to be a valuable tool for dereplication of these related compounds, and for the first time, five mono-rhamnolipids from a bacterium within the P. fluorescence group were characterized, including one new mono-rhamnolipid.

Tao, YW, Li PL, Zhang DJ, Glukhov E, Gerwick L, Zhang C, Murray TF, Gerwick WH.  2018.  Samholides, swinholide-related metabolites from a marine cyanobacterium cf. Phormidium sp. Journal of Organic Chemistry. 83:3034-3046.   10.1021/acs.joc.8b00028   AbstractWebsite

Cancer cell cytotoxicity was used to guide the isolation of nine new swinholide-related compounds, named samholides A-I (1-9), from an American Samoan marine cyanobacterium cf. Phormidium sp. Their structures were determined by extensive analysis of 1D and 2D NMR spectroscopic data. The new compounds share an unusual 20-demethyl 44-membered lactone ring composed of two monomers, and they demonstrate structural diversity arising from geometric isomerization of double bonds, sugar units with unique glyceryl moieties and varied methylation patterns. All of the new samholides were potently active against the H-460 human lung cancer cell line with IC50 values ranging from 170 to 910 nM. The isolation of these new swinholide-related compounds from a marine cyanobacterium reinvigorates questions concerning the evolution and biosynthetic origin of these natural products.

Shao, CL, Mou XF, Cao F, Spadafora C, Glukhov E, Gerwick L, Wang CY, Gerwick WH.  2018.  Bastimolide B, an antimalarial 24-membered marine macrolide possessing a tert-butyl group. Journal of Natural Products. 81:211-215.   10.1021/acs.jnatprod.7b00917   AbstractWebsite

We reported previously the discovery of the potent antimalarial 40-membered macrolide bastimolide A (1) from the tropical marine cyanobacterium Okeania hirsute. Continued investigation has led to the discovery of a new analogue, bastimolide B (2), a 24-membered polyhydroxy macrolide with a long aliphatic chain and unique terminal tertbutyl group. Its complete structure was determined by a combination of extensive spectroscopic methods and comparative analysis of its methanolysis products with those of bastimolide A. A methanolysis mechanism for bastimolide A is proposed, and one unexpected isomerization product of the C2-C3 double bond, 2-(E)-bastimolide A (3), was obtained. Bastimolide B (2) showed strong antimalarial activity against chloroquine-sensitive Plasmodium falciparum strain HB3. A preliminary investigation of the structure activity relationship based on six analogues revealed the importance of the double bond as well as the 1,3-diol and 1,3,5-triol functionalities.

Moss, NA, Leao T, Glukhov E, Gerwick L, Gerwick WH.  2018.  Collection, Culturing, and Genome Analyses of Tropical Marine Filamentous Benthic Cyanobacteria. Marine Enzymes and Specialized Metabolism, Pt A. 604( Moore BS, Ed.).:3-43., San Diego: Elsevier Academic Press Inc   10.1016/bs.mie.2018.02.014   Abstract

Decreasing sequencing costs has sparked widespread investigation of the use of microbial genomics to accelerate the discovery and development of natural products for therapeutic uses. Tropical marine filamentous cyanobacteria have historically produced many structurally novel natural products, and therefore present an excellent opportunity for the systematic discovery of new metabolites via the information derived from genomics and molecular genetics. Adequate knowledge transfer and institutional know-how are important to maintain the capability for studying filamentous cyanobacteria due to their unusual microbial morphology and characteristics. Here, we describe workflows, procedures, and commentary on sample collection, cultivation, genomic DNA generation, bioinformatics tools, and biosynthetic pathway analysis concerning filamentous cyanobacteria.

Skiba, MA, Sikkema AP, Moss NA, Tran CL, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL.  2017.  A mononuclear iron-dependent methyltransferase catalyzes initial steps in assembly of the apratoxin A polyketide starter unit. Acs Chemical Biology. 12:3039-3048.   10.1021/acschembio.7b00746   AbstractWebsite

Natural product biosynthetic pathways contain a plethora of enzymatic tools to carry out difficult biosynthetic transformations. Here, we discover an unusual mononuclear iron dependent methyltransferase that acts in the initiation steps of apratoxin A biosynthesis (AprA MT1). Fe3+-replete AprA MT1 catalyzes one or two methyl transfer reactions on the substrate malonyl-ACP (acyl carrier protein), whereas Co2+, Fe2+, Mn2+, and Ni2+ support only a single methyl transfer. MT1 homologues' exist;Within the "GNAT" (GCNS-related N-acetyltransferase) loading modules of several modular biosynthetic pathways with propionyl, isobutyryt or pivaloyl starter units. GNAT domains are thought to catalyze decarboXylation of malonyl-CoA and acetyl transfer to a carrier protein. In AprA, the GNAT domain lacks both decarboxylation and acyl transfer activity. A crystal structure of the AprA MT1-GNAT di-domain with bound Mn2+, malonate, and the methyl donor S-adenosylmethionine (SAM) reveals that the malonyl substrate is a bidentate metal ligand, indicating that the metal acts as a Lewis acid to promote methylation of the malonyl alpha-carbon. The GNAT domain is truncated relative to functional homologues. These results afford an expanded understanding of MT1-GNAT structure and activity arid permit the functional annotation of homologous GNAT loading modules both with and without methyltransferases, additionally revealing their rapid evolutionary adaptation in different biosynthetic contexts.

Zhang, C, Idelbayev Y, Roberts N, Tao YW, Nannapaneni Y, Duggan BM, Min J, Lin EC, Gerwick EC, Cottrell GW, Gerwick WH.  2017.  Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research. Scientific Reports. 7   10.1038/s41598-017-13923-x   AbstractWebsite

Various algorithms comparing 2D NMR spectra have been explored for their ability to dereplicate natural products as well as determine molecular structures. However, spectroscopic artefacts, solvent effects, and the interactive effect of functional group(s) on chemical shifts combine to hinder their effectiveness. Here, we leveraged Non-Uniform Sampling (NUS) 2D NMR techniques and deep Convolutional Neural Networks (CNNs) to create a tool, SMART, that can assist in natural products discovery efforts. First, an NUS heteronuclear single quantum coherence (HSQC) NMR pulse sequence was adapted to a state-of-the-art nuclear magnetic resonance (NMR) instrument, and data reconstruction methods were optimized, and second, a deep CNN with contrastive loss was trained on a database containing over 2,054 HSQC spectra as the training set. To demonstrate the utility of SMART, several newly isolated compounds were automatically located with their known analogues in the embedded clustering space, thereby streamlining the discovery pipeline for new natural products.

Gerwick, WH.  2017.  The Face of a Molecule. Journal of Natural Products. 80:2583-2588.   10.1021/acs.jnatprod.7b00624   AbstractWebsite

Recent technological advances in mass spectrometry and NMR spectroscopy have enabled new approaches for the rapid and insightful profiling of natural product mixtures. MALDI-MS with the provision of biosynthetic heavy-isotope labeled precursors can be a powerful method by which to interrogate a natural product metabolome and to gain insight into its unique constituents; this is illustrated herein by the detection, isolation, and characterization of cryptomaldamide. MS/MS-based Molecular Networks, facilitated by the Global Natural Products Social (GNPS) platform, is rapidly changing the way in which we dereplicate known natural products in mixtures, find new analogues in desired structure classes, and identify fundamentally new chemical entities. This method can be linked to genomic information to assist in genome-driven natural products discovery and is illustrated here with the characterization of the columbamides. Similarly, algorithmic interpretation of NMR data is facilitating the automatic identification or classification of new natural products. We developed such a tool named the Small Molecule Accurate Recognition Technology (SMART), which employs a convolutional neural network to classify HSQC spectra of organic molecules using pattern recognition principles. The discovery and rapid classification of several new peptides from a marine cyanobacterium as members of the viequeamide class provides an example of its utility in natural products research. These three illustrations represent different methods by which to look at the external features of a chemical substance and derive valuable insights into its identity or, as described herein, the "face of a molecule".

Fang, F, Zhao JY, Ding LJ, Huang CH, Naman CB, He S, Wu B, Zhu P, Luo QJ, Gerwick WH, Yan XJ, Wang QW, Zhang ZJ, Cui W.  2017.  5-Hydroxycyclopenicillone, a New beta-Amyloid Fibrillization Inhibitor from a Sponge-Derived Fungus Trichoderma sp HPQJ-34. Marine Drugs. 15   10.3390/md15080260   AbstractWebsite

A new cyclopentenone, 5-hydroxycyclopeni cillone (1), was isolated together with three known compounds, ar-turmerone (2), citreoisocoumarin (3), and 6-O-methyl-citreoisocoumarin (4), from a culture of the sponge-derived fungus Trichoderma sp. HPQJ-34. The structures of 1-4 were characterized using comprehensive spectroscopic analyses. The absolute configuration of 1 was determined by comparison of electronic circular dichroism (ECD) spectra with literature values used for the reported analogue, cyclopenicillone (5), which was not isolated in this research. Compound 1 was shown to scavenge 2,2-diphenyl-1-picrylhydrazyl free radicals, and decrease beta-amyloid (A beta) fibrillization in vitro. Moreover, 1 significantly reduced H2O2-induced neurotoxicity in SH-SY5Y cells. These findings suggested that compound 1, a newly discovered cyclopentenone, has moderate anti-oxidative, anti-A fi fibrillization properties and neuroprotective effects, and might be a good free radical scavenger.

Naman, CB, Almaliti J, Armstrong L, Caro-Diaz EJ, Pierce ML, Glukhov E, Fenner A, Spadafora C, Debonsi HM, Dorrestein PC, Murray TF, Gerwick WH.  2017.  Discovery and Synthesis of Caracolamide A, an Ion Channel Modulating Dichlorovinylidene Containing Phenethylamide from a Panamanian Marine Cyanobacterium cf. Symploca Species. Journal of Natural Products. 80:2328-2334.   10.1021/acs.jnatprod.7b00367   AbstractWebsite

A recent untargeted metabolomics investigation into the chemical profile of 10 organic extracts from cf. Symploca spp. revealed several interesting chemical leads for further natural product drug discovery. Subsequent target directed isolation efforts with one of these, a Panamanian marine cyanobacterium cf. Symploca sp., yielded a phenethylamide metabolite that terminates in a relatively rare gemdichlorovinylidene moiety, caracolarnide A (1), along with a known isotactic polymethoxy-1-alkene (2). Detailed NMR and HRESIMS analyses were used to determine the structures of these molecules, and compound 1 was confirmed by a three step synthesis. Pure compound 1 was shown to have in vitro calcium influx and calcium channel oscillation modulatory activity when tested as low as 10 pM using cultured murine cortical neurons, but was not cytotoxic to NCI-H460 human non-small-cell lung cancer cells in vitro (IC50 > 10 mu M).

Almaliti, J, Malloy KL, Glukhov E, Spadafora C, Gutierrez M, Gerwick WH.  2017.  Dudawalamides A-D, antiparasitic cyclic depsipeptides from the marine cyanobacterium Moorea producens. Journal of Natural Products. 80:1827-1836.   10.1021/acs.jnatprod.7b00034   AbstractWebsite

A family of 2,2-dimethyl-3-hydroxy-7-octynoic acid (Dhoya)-containing cyclic depsipeptides, named dudawalamides A-D (1-4), was isolated from a Papua New Guinean field collection of the cyanobacterium Moorea producens using bioassay-guided and spectroscopic approaches. The planar structures of dudawalamides A-D were determined by a combination of 1D and 2D NMR experiments and MS analysis, whereas the absolute configurations were determined by X-ray crystallography, modified Marfey's analysis, chiral-phase GCMS, and chiral-phase HPLC. Dudawalamides A-D possess a broad spectrum of antiparasitic activity with minimal mammalian cell cytotoxicity. Comparative analysis of the Dhoya-containing class of lipopeptides reveals intriguing structure-activity relationship features of these NRPS-PKS-derived metabolites and their derivatives.

Luzzatto-Knaan, T, Garg N, Wang MX, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandov T, Bandeira N, Gerwick WH, Dorrestein PC.  2017.  Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. Elife. 6   10.7554/eLife.24214   AbstractWebsite

Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium.

Kinnel, RB, Esquenazi E, Leao T, Moss N, Mevers E, Pereira AR, Monroe EA, Korobeynikov A, Murray TF, Sherman D, Gerwick L, Dorrestein PC, Gerwick WH.  2017.  A maldiisotopic approach to discover natural products: Cryptomaldamide, a hybrid tripeptide from the marine cyanobacterium Moorea producens. Journal of Natural Products. 80:1514-1521.   10.1021/acs.jnatprod.7b00019   AbstractWebsite

Genome sequencing of microorganisms has revealed a greatly increased capacity for natural products biosynthesis than was previously recognized from compound isolation efforts alone. Hence, new methods are needed for the discovery and description of this hidden secondary metabolite potential. Here we show that provision of heavy nitrogen N-15-nitrate to marine cyanobacterial cultures followed by single-filament MALDI analysis over a period of days was highly effective in identifying a new natural product with an exceptionally high nitrogen content. The compound, named cryptomaldamide, was subsequently isolated using MS to guide the purification process, and its structure determined by 2D NMR and other spectroscopic and chromatographic methods. Bioinformatic analysis of the draft genome sequence identified a 28.7 kB gene cluster that putatively encodes for cryptomaldamide biosynthesis. Notably, an amidinotransferase is proposed to initiate the biosynthetic process by transferring an amidino group from arginine to serine to produce the first residue to be incorporated by the hybrid NRPS-PKS pathway. The maldiisotopic approach presented here is thus demonstrated to provide an orthogonal method by which to discover novel chemical diversity from Nature.

Pye, CR, Bertin MJ, Lokey SR, Gerwick WH, Linington RG.  2017.  Retrospective analysis of natural products provides insights for future discovery trends. Proceedings of the National Academy of Sciences.   10.1073/pnas.1614680114   Abstract

Understanding of the capacity of the natural world to produce secondary metabolites is important to a broad range of fields, including drug discovery, ecology, biosynthesis, and chemical biology, among others. Both the absolute number and the rate of discovery of natural products have increased significantly in recent years. However, there is a perception and concern that the fundamental novelty of these discoveries is decreasing relative to previously known natural products. This study presents a quantitative examination of the field from the perspective of both number of compounds and compound novelty using a dataset of all published microbial and marine-derived natural products. This analysis aimed to explore a number of key questions, such as how the rate of discovery of new natural products has changed over the past decades, how the average natural product structural novelty has changed as a function of time, whether exploring novel taxonomic space affords an advantage in terms of novel compound discovery, and whether it is possible to estimate how close we are to having described all of the chemical space covered by natural products. Our analyses demonstrate that most natural products being published today bear structural similarity to previously published compounds, and that the range of scaffolds readily accessible from nature is limited. However, the analysis also shows that the field continues to discover appreciable numbers of natural products with no structural precedent. Together, these results suggest that the development of innovative discovery methods will continue to yield compounds with unique structural and biological properties.

Zhang, C, Naman CB, Engene N, Gerwick WH.  2017.  Laucysteinamide A, a hybrid PKS/NRPS metabolite from a Saipan cyanobacterium, cf. Caldora penicillata. Marine Drugs. 15   10.3390/md15040121   AbstractWebsite

A bioactivity guided study of a cf. Caldora penicillata species, collected during a 2013 expedition to the Pacific island of Saipan, Northern Mariana Islands (a commonwealth of the USA), led to the isolation of a new thiazoline-containing alkaloid, laucysteinamide A (1). Laucysteinamide A is a new monomeric analogue of the marine cyanobacterial metabolite, somocystinamide A (2), a disulfide-bonded dimeric compound that was isolated previously from a Fijian marine cyanobacterium. The structure and absolute configuration of laucysteinamide A (1) was determined by a detailed analysis of its NMR, MS, and CD spectra. In addition, the highly bioactive lipid, curacin D (3), was also found to be present in this cyanobacterial extract. The latter compound was responsible for the potent cytotoxicity of this extract to H-460 human non-small cell lung cancer cells in vitro.

Dhaneesha, M, Naman CB, Krishnan KP, Sinha RK, Jayesh P, Joseph V, Singh ISB, Gerwick WH, Sajeevan TP.  2017.  Streptomyces artemisiae MCCB 248 isolated from Arctic fjord sediments has unique PKS and NRPS biosynthetic genes and produces potential new anticancer natural products. 3 Biotech. 7   10.1007/s13205-017-0610-3   AbstractWebsite

After screening marine actinomycetes isolated from sediment samples collected from the Arctic fjord Kongsfjorden for potential anticancer activity, an isolate identified as Streptomyces artemisiae MCCB 248 exhibited promising results against the NCI-H460 human lung cancer cell line. H460 cells treated with the ethyl acetate extract of strain MCCB 248 and stained with Hoechst 33342 showed clear signs of apoptosis, including shrinkage of the cell nucleus, DNA fragmentation and chromatin condensation. Further to this treated cells showed indications of early apoptotic cell death, including a significant proportion of Annexin V positive staining and evidence of DNA damage as observed in the TUNEL assay. Amplified PKS 1 and NRPS genes involved in secondary metabolite production showed only 82% similarity to known biosynthetic genes of Streptomyces, indicating the likely production of a novel secondary metabolite in this extract. Additionally, chemical dereplication efforts using LC-MS/MS molecular networking suggested the presence of a series of undescribed tetraene polyols. Taken together, these results revealed that this Arctic S. artemisiae strain MCCB 248 is a promising candidate for natural products drug discovery and genome mining for potential anticancer agents.

Leao, T, Castelao G, Korobeynikov A, Monroe EA, Podell S, Glukhov E, Allen EE, Gerwick WH, Gerwick L.  2017.  Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea. Proceedings of the National Academy of Sciences of the United States of America. 114:3198-3203.   10.1073/pnas.1618556114   AbstractWebsite

Cyanobacteria are major sources of oxygen, nitrogen, and carbon in nature. In addition to the importance of their primary metabolism, some cyanobacteria are prolific producers of unique and bioactive secondary metabolites. Chemical investigations of the cyanobacterial genus Moorea have resulted in the isolation of over 190 compounds in the last two decades. However, preliminary genomic analysis has suggested that genome-guided approaches can enable the discovery of novel compounds from even well-studied Moorea strains, highlighting the importance of obtaining complete genomes. We report a complete genome of a filamentous tropical marine cyanobacterium, Moorea producens PAL, which reveals that about one-fifth of its genome is devoted to production of secondary metabolites, an impressive four times the cyanobacterial average. Moreover, possession of the complete PAL genome has allowed improvement to the assembly of three other Moorea draft genomes. Comparative genomics revealed that they are remarkably similar to one another, despite their differences in geography, morphology, and secondary metabolite profiles. Gene cluster networking highlights that this genus is distinctive among cyanobacteria, not only in the number of secondary metabolite pathways but also in the content of many pathways, which are potentially distinct from all other bacterial gene clusters to date. These findings portend that future genome-guided secondary metabolite discovery and isolation efforts should be highly productive.

Naman, CB, Rattan R, Nikoulina SE, Lee J, Miller BW, Moss NA, Armstrong L, Boudreau PD, Debonsi HM, Valeriote FA, Dorrestein PC, Gerwick WH.  2017.  Integrating molecular networking and biological assays to target the isolation of a cytotoxic cyclic octapeptide, Samoamide A, from an American Samoan marine cyanobacterium. Journal of Natural Products. 80:625-633.   10.1021/acsjnatprod.6600907   AbstractWebsite

Integrating LC-MS/MS molecular networking and bioassay-guided fractionation enabled the targeted isolation of a new and bioactive cyclic octapeptide, samoamide A (1), from a sample of cf. Symploca sp. collected in American Samoa. The structure of 1 was established by detailed 1D and 2D NMR experiments, HRESIMS data, and chemical degradation/chromatographic (e.g., Marfey's analysis) studies. Pure compound 1 was shown to have in vitro cytotoxic activity against several human cancer cell lines in both traditional cell culture and zone inhibition bioassays. Although there was no particular selectivity between the cell lines tested for samoamide A, the most potent activity was observed against H460 human non-small-cell lung cancer cells (IC50 = 1.1 mu M). Molecular modeling studies suggested that one possible mechanism of action for 1 is the inhibition of the enzyme dipeptidyl peptidase (CD26, DPP4) at a reported allosteric binding site, which could lead to many downstream pharmacological effects. However, this interaction was moderate when tested in vitro at up to 10 mu M and only resulted in about 16% peptidase inhibition. Combining bioassay screening with the cheminformatics strategy of LC-MS/MS molecular networking as a discovery tool expedited the targeted isolation of a natural product possessing both a novel chemical structure and a desired biological activity.

Sabry, OM, Goeger DE, Gerwick WH.  2017.  Biologically active new metabolites from a Florida collection of Moorea producens. Natural Product Research. 31:555-561.   10.1080/14786419.2016.1207074   AbstractWebsite

A bioassay-guided investigation (cancer cell cytotoxicity) of a Moorea producens collection from Key West, Florida, led to the discovery of two new bioactive natural products [(+)-malyngamide Y and a cyclic depsipeptide, (+)-floridamide]. Their planar structures were deduced through extensive analysis of 1D and 2D NMR spectroscopic data and supported by HRFAB mass spectrometry. The new cyclic depsipeptide contains four amino acids units, including N- methyl phenylalanine, proline, valine and alanine, beside the unique unit, 2,2-dimethyl-3hydroxy- octanoic acid. In addition to the discovery of these two new compounds, two previously reported metabolites were also isolated and identified from this cyanobacterial collection; (-)-C-12 lyngbic acid and the antibacterial agent (-)-malyngolide.

Sabry, OMM, Goeger DE, Valeriote FA, Gerwick WH.  2017.  Cytotoxic halogenated monoterpenes from Plocamium cartilagineum. Natural Product Research. 31:261-267.   10.1080/14786419.2016.1230115   AbstractWebsite

As a result of our efforts to identify bioactive agents from marine algae, we have isolated and identified one new halogenated monoterpene 1 [(-)-(5E,7Z)-348-trichloro-7-dichloromethyl-3-methyl-157-octatriene] in addition to three known compounds (2, 3 and 4) from the red alga Plocamium cartilagineum collected by hand from the eastern coast of South Africa. Compound 1 was found to be active as a cytotoxic agent in human lung cancer (NCI-H460) and mouse neuro-2a cell lines (IC50 4g/mL). Two of these compounds (3 and 4) were found to have cytotoxic activity in other cell line assays, especially against human leukaemia and human colon cancers (IC50 1.3g/mL). None of these metabolites were active as sodium channel blockers or activators. All structures were determined by spectroscopic methods (UV, IR, LRMS, HRMS, 1D NMR and 2D NMR). 1D and 2D NOE experiments were carried out on these compounds to confirm the geometry of the double bonds. [GRAPHICS] .