NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products.

Computational approaches such as genome and metabolome mining are becoming essential to natural products (NPs) research. Consequently, a need exists for an automated structure-type classification system to handle the massive amounts of data appearing for NP structures. An ideal semantic ontology for the classification of NPs should go beyond the simple presence/absence of chemical substructures, but also include the taxonomy of the producing organism, the nature of the biosynthetic pathway, and/or their biological properties. Thus, a holistic and automatic NP classification framework could have considerable value to comprehensively navigate the relatedness of NPs, and especially so when analyzing large numbers of NPs. Here, we introduce NPClassifier, a deep-learning tool for the automated structural classification of NPs from their counted Morgan fingerprints. NPClassifier is expected to accelerate and enhance NP discovery by linking NP structures to their underlying properties.

Alkaloids from Corydalis decumbens suppress neuronal excitability in primary cultures of mouse neocortical neurons.

Eight previously undescribed alkaloids, named corydemine, dihydrocorydemine, corydedine, 8,13-dioxo-14-hydroxytetrahydropalmatine, egenine-α-N-oxide, egenine-ß-N-oxide, 7'-O-ethylegenine-α-N-oxide, and 7'-O-ethylegenine-ß-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 µM, respectively.

5-Hydroxycyclopenicillone, a New ß-Amyloid Fibrillization Inhibitor from a Sponge-Derived Fungus Trichoderma sp. HPQJ-34.

Abstract: 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 ß-amyloid (Aß) 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-Aß fibrillization properties and neuroprotective effects, and might be a good free radical scavenger.

Uprolides N, O and P from the Panamanian Octocoral Eunicea succinea.

Three new diterpenes, uprolide N (1), uprolide O (2), uprolide P (3) and a known one, dolabellane (4), were isolated from the CH2Cl2-MeOH extract of the gorgonian octocoral Eunicea succinea, collected from Bocas del Toro, on the Caribbean coast of Panama. Their structures were determined using spectroscopic analyses, including 1D and 2D NMR and high-resolution mass spectrometry (HRMS) together with molecular modeling studies. Compounds 1-3 displayed anti-inflammatory properties by inhibiting production of Tumor Necrosis Factor (TNF) and Interleukin (IL)-6 induced by lipopolysaccharide (LPS) in murine macrophages.

Molecular networking as a dereplication strategy.

A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogues, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogues.

Antiparasitic and anticancer constituents of the endophytic fungus Aspergillus sp. strain F1544.

With the combined goal of finding the best anti-parasitic and anti-cancer activities as well as isolating the bioactive agents and studying their structures and biological properties, we proceeded to perform a small-scale cultivation of Aspergillus sp. strain F1544 using Potato Dextrose, Malt Extract, Czapek Dox and Eight Vegetables media. From the more promising extracts (obtaining using potato dextrose and czapek dox media in large scale) of this fungus, we isolated the five compounds: pseurotin A (1), 14-norpseurotin A (2), FD-838 (3), and pseurotin D (4), and fumoquinone B (5). All compounds showed good antileishmanial and moderate anticancer activities.

Screening and evaluation of antiparasitic and in vitro anticancer activities of Panamanian endophytic fungi.

Many compounds produced by fungi have relevant pharmaceutical applications. The purpose of this study was to collect and isolate endophytic fungi from different regions of Panama and then to test their potential therapeutic activities against Leishmania donovani, Plasmodium falciparum, and Trypanosoma cruzi as well as their anticancer activities in MCF-7 cells. Of the 25 fungal isolates obtained, ten of them had good anti-parasitic potential, showing selective activity against L. donovani; four had significant anti-malarial activity; and three inhibited the growth of T. cruzi. Anticancer activity was demonstrated in four isolates. Of the active isolates, Edenia sp. strain F0755, Xylaria sp. strain F1220, Aspergillus sp. strain F1544, Mycoleptodiscus sp. strain F0194, Phomopsis sp. strain F1566, Pycnoporus sp. strain F0305, and Diaporthe sp. strain F1647 showed the most promise based on their selective bioactivity and lack of toxicity in the assays.

Chemical constituents of the new endophytic fungus Mycosphaerella sp. nov. and their anti-parasitic activity.

Chemical investigation of a new endophytic fungus, Mycosphaerella sp. nov. strain F2140, associated with the foliage of the plant Psychotria horizontalis (Rubiaceae) in Panama, resulted in the isolation of cercosporin (1) and a new cercosporin analog (3) as the major components. The structures of minor compounds in the extract were elucidated by detailed spectroscopic analysis as 2-(2-butyl)-6-ethyl-3-hydroxy-6-methylcyclohex-2-ene-1,5-dione (4), 3-(2-butyl)-6-ethyl-5-hydroxy-2-methoxy-6-methyl-cyclohex-2-enone (5), and an isomer of 5 (6). To study the influence of the hydroxy groups on the anti-parasitic activity of cercosporin, compound 1 was acetylated to obtain derivative 2. The isolated compounds 1- 6 were tested in vitro to determine their anti-parasitic activity against the causal agents of malaria (Plasmodium falciparum), leishmaniasis (Leishmania donovani), and Chagas disease (Trypanosoma cruzi). Cytotoxicity and potential anticancer activity of these compounds were evaluated using mammalian Vero cells and MCF7 cancer cell lines, respectively. Compounds 1 and 2 displayed high potency against L. donovani (IC50 0.46 and 0.64 microM), T. cruzi (IC50 1.08 and 0.78 microM), P. falciparum (IC50 1.03 and 2.99 microM), and MCF7 cancer cell lines (IC50 4.68 and 3.56 microM). Compounds 3-6 were not active in these assays at a concentration of 10 microg/mL.

Hydroxyalkenylresorcinols from Stylogyne turbacensis.

Two new compounds, 5-(11'(S)-hydroxy-8'-heptadecenyl)resorcinol (3) and 5-(12'(S)-hydroxy-8',14'-heptadecadienyl)resorcinol (4), were isolated from the leaves of Stylogyne turbacensis together with the known analogue metabolites 1 and 2. Compounds 3 and 4 showed the strongest activity in the leishmania assay, 7 and 3 microM, respectively, while compounds 1, 2, and 4 showed moderate activity against a drug-resistant strain of Trypanosoma cruzi with IC(50) values of 30, 25, and 22 microM, respectively. Additional testing in MCF-7 and NCI-H460 was performed for compounds 3 and 4. The structures of compounds 1-4 were elucidated using NMR, MS, and other spectroscopic data. The absolute stereochemistry of compounds 3 and 4 was also investigated using the Mosher ester approach. Peracetylated derivatives of these four metabolites were produced and their activities determined in the Trypanosoma cruzi assay.

Weakly antimalarial flavonol arabinofuranosides from Calycolpus warszewiczianus.

Three new flavonol arabinosides (2-4) were isolated from the young leaves of Calycolpus warszewiczianus. The structures were determined as myricetin-3-O-alpha-L-3' '-acetylarabinofuranoside (2), myricetin-3-O-alpha-L-3' ',5' '-diacetylarabinofuranoside (3), and 5-galloylquercetin-3-O-alpha-L-arabinofuranoside (4). Molecular structures were elucidated using NMR spectroscopy in combination with IR and MS data. Two known compounds, myricetin-3-O-alpha-L-arabinofuranoside (1) and (-)-epi-catechin (5), were also isolated. The compounds were tested in vitro against a chloroquine-resistant strain of Plasmodium falciparum, Leishmania mexicana, and Trypanosoma cruzi parasites. Compound 4 demonstrated weak activity against a chloroquine-resistant strain of P. falciparum (14.5 microM), whereas none of the compounds demonstrated activity against L. mexicana and T. cruzi at the concentrations of 40 and 50 microg/mL, respectively, and no cytotoxicity was detected against mammalian cells below 100 microg/mL.

Minor alkaloids from Guatteria dumetorum with antileishmanial activity.

Nine known alkaloids [(+)-isodomesticine (1), (+)-norisodomesticine (2), (+)-nantenine ( 3), (+)-neolitsine (4), (+)-lirioferine (5), (+)-N-methyllaurotetanine (6), (+)-norlirioferine (7), (+)-isoboldine (8) and (+)-reticuline (9)] were isolated from young leaves of Guatteria dumetorum. Their structures were confirmed by NMR, mass and UV spectral analysis and by comparison to literature data. The growth inhibitory activity of each alkaloid was determined against the parasite Leishmania mexicana. Compounds 1-4 all showed significant activity whereby potency increased when a methylenedioxy functionality was present, especially at the 1,2-positions.

Secondary metabolites from marine cyanobacteria and algae inhibit LFA-1/ICAM-1 mediated cell adhesion.

An assay for inhibitors of LFA-1/ICAM-1 mediated cell-cell adhesion has been employed to identify new pharmacologically active compounds from marine cyanobacteria and algae. From a panel of sixty unusual marine natural products, seventeen compounds inhibited LFA-1/ICAM-1-based cell aggregation without showing significant cytotoxicity in the primary assay. Six compounds inhibited the cell-cell adhesion of HL-60 cells to CHO-ICAM-1 cells. The unusual oxylipin Cymathere aldehyde methyl ester (IC (50) 3.5 microM), cyanobacterial lipopeptides microcolins B (IC (50) 0.15 microM) and D (IC (50) 0.9 microM), bromophenol avrainvilleol (IC (50) 2.2 microM), sesquiterpene cymopol (IC (50) 2.7 microM), and cryptophyte derived compound styrylchromone hormothamnione diacetate (IC (50) 1.5 microM) significantly inhibited LFA-1/ICAM-1 mediated cell adhesion. The pharmacological activity and structure-activity relationships of selected marine algal metabolites are described. Abbreviations. LFA-1:Lymphocyte function-associated molecule-1 ICAM-1:Intercellular cell adhesion molecule-1 PMA:Phorbol 12-myristate 13-acetate HL-60:Promyelocytic human leukemia-60 CHO:Chinese hamster ovary

Evaluation of the efficiency of three different solvent systems to extract triterpene saponins from roots of Panax quinquefolius using high-performance liquid chromatography.

Despite the wide availability of liquid herbal extracts using mixtures of alcohol, glycerin, and water, or glycerin and water as solvents, no data on the chemical composition of such extracts is readily available. In this study, the amount and the stability of the major saponins in Panax quinquefolius root extracts, made either with 50% (v/v) aqueous ethanol, a mixture (v/v/v) of 20% ethanol, 40% glycerin, and 40% water, or with 65% (v/v) aqueous glycerin, were evaluated by HPLC-UV analysis. The amount of total saponins was highest in the 50% aqueous ethanol extract (61.7 +/- 0.1 mg/g dry root), although similar to the ethanol-glycerin-water extract (59.4 +/- 0.5 mg/g dry root). Saponins were significantly lower in the 65% aqueous glycerin extract (51.5 +/- 0.2 mg/g dry root). Interestingly, the amounts of individual saponins were quite variable depending on the solvent. This is in part due to enzymatic cleavage of ginsenosides in the glycerin containing extracts during the maceration process. Storage of the extracts at 25 degrees C over the period of a year led to a 13-15% loss of saponins with all three types of extractions.

Polyenoic fatty acid isomerase from the marine alga Ptilota filicina: protein characterization and functional expression of the cloned cDNA.

The recently described enzyme, polyenoic fatty acid isomerase (PFI), from the marine alga Ptilota filicina J. Argardh has been analyzed with respect to its protein structure and an associated cofactor. The enzyme was purified to homogeneity (as judged by SDS-PAGE and silver staining). By sedimentation equilibrium ultracentrifugation the mass of the native enzyme was estimated to be 125 kDa. The N-terminal peptide sequence derived from this protein was used to isolate two very similar cDNA clones encoding novel 500-amino acid proteins, both with calculated molecular masses of 55.9 kDa and pIs of 4.87. The data predict translation of a preprotein containing a signal peptide of 21 amino acids that is removed during maturation. Deglycosylation assays demonstrate that native PFI from P. filicina is a glycoprotein. The purified protein is chromophoric with a flavin-like UV spectrum and sequence analysis reveals the presence of a flavin-binding motif near the mature N-terminus. Heterologous expression of active PFI in Arabidopsis, using one of the cDNA clones, was successful as evidenced by conversion of arachidonic acid to a conjugated triene in an in vitro assay of the transgenic plant tissues.