Integrating Taxonomic and Chemical Diversity of Mangrove-Associated Ascomycetes to Discover or Repurpose Bioactive Natural Products.

Natural product reisolation is a bottleneck when discovering new bioactive chemical entities from nature. To overcome this issue, multi-informative approaches integrating several layers of data have been applied with promising results. In this study, integration of taxonomy, nontargeted metabolomics, and bioactivity information resulted in the selection of Scytalidium sp. IQ-074 and Diaporthe sp. IQ-053 to isolate new natural products active against hPTP1B1-400 and repurpose others as antibiotics. Strain IQ-074 was selected based on the hypothesis that investigating poorly studied and highly metabolic taxa could lead to the isolation of new chemical entities. A chemical investigation of IQ-074 resulted in the isolation of papyracillic acid A (14), 7-deoxypapyracillic acid A (15a and 15b), and linear polyketides scytalpolyols A-D (16-19). Compound 17 inhibited hPTP1B1-400 with a half-maximal inhibitory concentration of 27.0 ± 1.7 µM. Diaporthe sp. IQ-053 was selected based on its antibacterial properties against pathogenic strains. Its chemical investigation yielded dothiorelones A (20) and I (21), cytosporones B (22) and C (23), pestalotiopsone B (24), and diaporthalasin (25). Compounds 22 and 25 inhibited the growth of Staphylococcus aureus and Staphylococcus epidermidis 42R and moderately inhibited the growth of Acinetobacter baumannii A564, a pandrug-resistant bacterium.

Absolute configuration and protein tyrosine phosphatase 1B inhibitory activity of xanthoepocin, a dimeric naphtopyrone from Penicillium sp. IQ-429.

Protein tyrosine phosphatase 1B (PTP1B) is an active target for developing drugs to treat type II diabetes, obesity, and cancer. However, in the past, research programs targeting this enzyme focused on discovering inhibitors of truncated models (hPTP1B1-282, hPTP1B1-298, or hPTP1B1-321), losing valuable information about the ligands' mechanism of inhibition and selectivity. Nevertheless, finding an allosteric site in hPTP1B1-321, and the full-length (hPTP1B1-400) protein expression, have shifted the strategies to discover new PTP1B inhibitors. Accordingly, as part of a research program directed at finding non-competitive inhibitors of hPTP1B1-400 from Pezizomycotina, the extract of Penicillium sp. (IQ-429) was chemically investigated. This study led to xanthoepocin (1) isolation, which was elucidated by means of spectroscopic and spectrometric data. The absolute configuration of 1 was determined to be 7R8S9R7'R8'S9'R by comparing the theoretical and experimental ECD spectra and by GIAO-NMR DP4 + statistical analysis. Xanthoepocin (1) inhibited the phosphatase activity of hPTP1B1-400 (IC50 value of 8.8 ± 1.0 µM) in a mixed type fashion, with ki and αki values of 5.5  and 6.6 µM, respectively. Docking xanthoepocin (1) with a homologated model of hPTP1B1-400 indicated that it binds in a pocket different from the catalytic triad at the interface of the N and C-terminal domains. Molecular dynamics (MD) simulations showed that 1 locks the WPD loop of hPTP1B1-400 in a closed conformation, avoiding substrate binding, products release, and catalysis, suggesting an allosteric modulation triggered by large-scale conformational and dynamics changes. Intrinsic quenching fluorescence experiments indicated that 1 behaves like a static quencher of hPTP1B1-400 (KSV = 1.1 × 105 M-1), and corroborated that it binds to the enzyme with an affinity constant (ka) of 3.7 × 105 M-1. Finally, the drug-likeness and medicinal chemistry friendliness of 1 were predicted with SwissADME.

One-step partial synthesis of (±)-asperteretone B and related hPTP1B1-400 inhibitors from butyrolactone I.

Protein tyrosine phosphatase 1B (PTP1B) is a validated target for developing antiobesity, antidiabetic and anticancer drugs. Over the past years, several inhibitors of PTP1B have been discovered; however, none has been approved by the drug regulatory agencies. Interestingly, the research programs focused on discovering PTP1B inhibitors typically use truncated structures of the protein (PTP1B1-300, 1-300 amino acids), leading to the loss of valuable information about the inhibition and selectivity of ligands and repeatedly misleading the optimization of putative drug leads. Up to date, only six inhibitors of the full-length protein (hPTP1B1-400), with affinity constants ranging from 1.3 × 104 to 3.3 × 106 M-1, have been reported. Towards the discovery of new ligands of the full-length human PTP1B (hPTP1B1-400) from natural sources, herein we describe the isolation of a γ-lactone (1, butyrolactone I) from the fungus Aspergillus terreus, as well as the semisynthesis, inhibitory properties (in vitro and in silico), and the structure-activity relationship of a set of butyrolactone derivatives (1 and 2, and 6-12) as hPTP1B1-400 inhibitors, as well as the affinity constant (ka = 2.2 × 105 M-1) of the 1-hPTP1B1-400 complex, which was determined by fluorescence quenching experiments, after the inner filter effect correction.

Dimeric phenalenones from Talaromyces sp. (IQ-313) inhibit hPTP1B1-400: Insights into mechanistic kinetics from in vitro and in silico studies.

A critical biological event that contributes to the appearance and progress of cancer and diabetes is the reversible phosphorylation of proteins, a process controlled by protein tyrosine-kinases (PTKs) and protein tyrosine-phosphatases (PTPs). Within the PTPs, PTP1B has gained significant interest since it is a validated target in drug discovery. Indeed, several PTP1B inhibitors have been developed, from both, synthesis and natural products. However, none have been approved by the FDA, due to their poor selectivity and/or pharmacokinetic properties. One of the most significant challenges to the discovery of PTP1B inhibitors (in vitro or in silico) is the use of truncated structures (PTP1B1-300), missing valuable information about the mechanisms of inhibition, and selectivity of ligands. The present study describes the biochemical characterization of a full-length PTP1B (hPTP1B1-400), as well as the description of phenalenones 1-4 and ursolic acid (5) as allosteric modulators. Compounds 1-5 showed inhibitory potential on hPTP1B1-400, with IC50 values ranging from 12.7 to 82.1 µM. Kinetic studies showed that 1 and 5 behave as mixed and non-competitive inhibitors, respectively. Circular dichroism experiments confirmed that 1 and 5 induced conformational changes to hPTP1B1-400. Further insights into the structure of hPTP1B1-400 were obtained from a homology model, which pointed out that the C-terminus (residues 301-400) is highly disordered. Molecular docking with the homologated model suggested that compounds 1 and 3-5 bind to the C-terminal domain, likely inducing conformational changes on the protein. Docking positions of compounds 1, 4, and 5 were refined with molecular dynamics simulations. Importantly, these simulations confirmed the high flexibility of the C-terminus of hPTP1B1-400, as well as the changes to its rigidity when bound to 1, 4, and 5.

A Review of the Ephedra genus: Distribution, Ecology, Ethnobotany, Phytochemistry and Pharmacological Properties.

Ephedra is one of the largest genera of the Ephedraceae family, which is distributed in arid and semiarid regions of the world. In the traditional medicine from several countries some species from the genus are commonly used to treat asthma, cold, flu, chills, fever, headache, nasal congestion, and cough. The chemical constituents of Ephedra species have been of research interest for decades due to their contents of ephedrine-type alkaloids and its pharmacological properties. Other chemical constituents such as phenolic and amino acid derivatives also have resulted attractive and have provided evidence-based supporting of the ethnomedical uses of the Ephedra species. In recent years, research has been expanded to explore the endophytic fungal diversity associated to Ephedra species, as well as, the chemical constituents derived from these fungi and their pharmacological bioprospecting. Two additional aspects that illustrate the chemical diversity of Ephedra genus are the chemotaxonomy approaches and the use of ephedrine-type alkaloids as building blocks in organic synthesis. American Ephedra species, especially those that exist in Mexico, are considered to lack ephedrine type alkaloids. In this sense, the phytochemical study of Mexican Ephedra species is a promising area of research to corroborate their ephedrine-type alkaloids content and, in turn, discover new chemical compounds with potential biological activity. Therefore, the present review represents a key compilation of all the relevant information for the Ephedra genus, in particular the American species, the species distribution, their ecological interactions, its ethnobotany, its phytochemistry and their pharmacological activities and toxicities, in order to promote clear directions for future research.

neo-Clerodane Diterpenoids from Salvia polystachya Stimulate the Expression of Extracellular Matrix Components in Human Dermal Fibroblasts.

Eleven neo-clerodane diterpenoids (1-11) including the new analogues 1, 2, and 10, and 3',5,6,7-tetrahydroxy-4'-methoxyflavone (12) were isolated from the aerial parts of Salvia polystachya. Polystachyne G (1) and 15-epi-polystachyne G (2) were isolated as an epimeric mixture, containing a 5-hydroxyfuran-2(5H)-one unit in the side chain at C-12 of the neo-clerodane framework. Polystachyne H (10) contains a 1(10),2-diene moiety and a tertiary C-4 hydroxy group. The structures of these compounds were established by analysis of their NMR spectroscopic and MS spectrometric data. The absolute configurations of compounds 3, 4, and 10 were determined through single-crystal X-ray diffraction analysis. The antibacterial, antifungal, and phytotoxic activities of the diterpenoids were determined. In addition, the stimulatory effect of the expression of extracellular matrix components of nine of the isolates (1-8 and 11) was assayed. Compounds 1-4, 8, and 11 increased the expression of the genes codifying for type I, type III, and type V collagens and for elastin.

Unraveling the antimicrobial activity of CuS functionalized titanates under visible LED light irradiation.

Titanate nanotubes (TNs) functionalized with CuS nanoparticles using the microwave-assisted hydrothermal method were characterized via XRD, Raman spectroscopy, UV-Vis spectrophotometry, and N2 physisorption. The as-synthesized CuS/TNs had anatase as the main crystalline phase and the band-gap energy was in the visible region, 2.9 eV. The TNs were recrystallized on titania and functionalized with CuS, forming spherical bundles. SEM showed agglomerates of cauliflower-like semispherical particles. The antimicrobial photoactive assets were evaluated against the bacteria Staphylococcus aureus and Escherichia coli. Inhibition was clearly visible in S. aureus after the first 20 min of exposure to a 6-W LED irradiation lamp. The visible-light catalyzed completely and irreversibly the inactivation of S. aureus after 60 min, however, in the case of E. coli, this material only slightly disturbed its growth, which was recovered after 60 min. The successful result obtained with S. aureus can be explained by the fact that it lacks periplasmic superoxide dismutase (SOD) but has staphyloxanthin for external protection against ROS. However, the CuS/TN particles could release Cu2+ ions, which got attached to bacterium structures or entered the cytoplasm; these events together with the generation of ROS under visible LED light helped inactivate quickly staphyloxanthin, thus inflicting permanent damage to the periplasmic membrane.

Nitrogen-fixing and uricolytic bacteria associated with the gut of Dendroctonus rhizophagus and Dendroctonus valens (Curculionidae: Scolytinae).

The bark beetles of the genus Dendroctonus feed on phloem that is a nitrogen-limited source. Nitrogen fixation and nitrogen recycling may compensate or alleviate such a limitation, and beetle-associated bacteria capable of such processes were identified. Raoultella terrigena, a diazotrophic bacteria present in the gut of Dendroctonus rhizophagus and D. valens, exhibited high acetylene reduction activity in vitro with different carbon sources, and its nifH and nifD genes were sequenced. Bacteria able to recycle uric acid were Pseudomonas fluorescens DVL3A that used it as carbon and nitrogen source, Serratia proteomaculans 2A CDF and Rahnella aquatilis 6-DR that used uric acid as sole nitrogen source. Also, this is the first report about the uric acid content in whole eggs, larvae, and adults (male and female) samples of the red turpentine beetle (Dendroctonus valens). Our results suggest that the gut bacteria of these bark beetles could contribute to insect N balance.

Phenotypic and Genomic Characterization of Streptomyces pakalii sp. nov., a Novel Species with Anti-Biofilm and Anti-Quorum Sensing Activity in ESKAPE Bacteria.

The increasing number of infections caused by antimicrobial multi-resistant microorganisms has led to the search for new microorganisms capable of producing novel antibiotics. This work proposes Streptomyces pakalii sp. nov. as a new member of the Streptomycetaceae family. The strain ENCB-J15 was isolated from the jungle soil in Palenque National Park, Chiapas, Mexico. The strain formed pale brown, dry, tough, and buried colonies in the agar with no diffusible pigment in GAE (glucose-asparagine-yeast extract) medium. Scanning electron micrographs showed typical mycelium with long chains of smooth and oval-shaped spores (3-10 m). The strain grew in all of the International Streptomyces Project (ISP)'s media at 28-37 °C with a pH of 6-9 and 0-10% NaCl. S. pakalii ENCB-J15 assimilated diverse carbon as well as organic and inorganic nitrogen sources. The strain also exhibited significant inhibitory activity against the prodigiosin synthesis of Serratia marcescens and the inhibition of the formation and destruction of biofilms of ESKAPE strains of Acinetobacter baumannii and Klebsiella pneumoniae. The draft genome sequencing of ENCB-J15 revealed a 7.6 Mb genome with a high G + C content (71.6%), 6833 total genes, and 6746 genes encoding putative proteins. A total of 26 accessory clusters of proteins associated with carbon sources and amino acid catabolism, DNA modification, and the antibiotic biosynthetic process were annotated. The 16S rRNA gene phylogeny, core-proteome phylogenomic tree, and virtual genome fingerprints support that S. pakalii ENCB-J15 is a new species related to Streptomyces badius and Streptomyces globisporus. Similarly, its average nucleotide identity (ANI) (96.4%), average amino acid identity (AAI) (96.06%), and virtual DNA-DNA hybridization (67.3%) provide evidence to recognize it as a new species. Comparative genomics revealed that S. pakalli and its closest related species maintain a well-conserved genomic synteny. This work proposes Streptomyces pakalii sp. nov. as a novel species that expresses anti-biofilm and anti-quorum sensing activities.

Gut-associated bacteria throughout the life cycle of the bark beetle Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) and their cellulolytic activities.

Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) is an endemic economically important insect of the Sierra Madre Occidental in Mexico. This bark beetle has an atypical behavior within the genus because just one beetle couple colonizes and kills seedlings and young trees of 11 pine species. In this work, the bacteria associated with the Dendroctonus rhizophagus gut were analyzed by culture-dependent and culture-independent methods. Analysis of 16S rRNA sequences amplified directly from isolates of gut bacteria suggests that the bacterial community associated with Dendroctonus rhizophagus, like that of other Dendroctonus spp. and Ips pini, is limited in number. Nine bacterial genera of γ-Proteobacteria and Actinobacteria classes were detected in the gut of Dendroctonus rhizophagus. Stenotrophomonas and Rahnella genera were the most frequently found bacteria from Dendroctonus rhizophagus gut throughout their life cycle. Stenotrophomonas maltophilia, Ponticoccus gilvus, and Kocuria marina showed cellulolytic activity in vitro. Stenotrophomonas maltophilia, Rahnella aquatilis, Raoultella terrigena, Ponticoccus gilvus, and Kocuria marina associated with larvae or adults of Dendroctonus rhizophagus could be implicated in nitrogen fixation and cellulose breakdown, important roles associated to insect development and fitness, especially under the particularly difficult life conditions of this beetle.

Elemenolides from Zinnia peruviana and evaluation of their antibacterial and α-glucosidase inhibitory activities.

A phytochemical study from Zinnia peruviana L. resulted in the isolation of a new elemene-type sesquiterpene lactone, zinaflorin VI (1), along with the known elemenolides 2-5 and the flavone onopordin (6). The structures of these compounds were determined by analysis of their spectroscopic data. The antibacterial activity of the γ-elemenolides 1, 4, and 5 was evaluated. The δ-elemenolide juniperin (7), previously isolated from Zinnia juniperifolia, was included in this assay. Compounds 1 and 7 were active against Bacillus subtilis and Staphylococcus aureus with MICs = 32 and 64 µg/mL for compound 1 and MICs = 4 and 8 µg/mL for compound 7. The α-glucosidase inhibitory activity of compounds 1, and 4-7 was evaluated, but none of these compounds was found to be active.

Further galphimines from a new population of Galphimia glauca.

Both DNA barcoding and phylogenetic data of the studied botanical material suggested the existence a new population of Galphimia glauca. Their leaves afforded three new nor-3,4-seco-friedelanes named galphimines M-O, together with known galphimines D, E, G, and I. Galphimines M and N possess bicyclic orthoacetates which are the first examples of orthoesters found in the Malpighiaceae family, while galphimine O has a 27,20-δ-lactone moiety. The structures elucidation followed from spectroscopic means and the absolute configuration followed from single crystal X-ray diffraction analyses. Tests for antibacterial and antifungal activities of galphimines N and M showed no promising effects.

Determining the scale at which variation in a single gene changes population yields.

Plant trait diversity is known to influence population yield, but the scale at which this happens remains unknown: divergent individuals might change yields of immediate neighbors (neighbor scale) or of plants across a population (population scale). We use Nicotiana attenuata plants silenced in mitogen-activated protein kinase 4 (irMPK4) - with low water-use efficiency (WUE) - to study the scale at which water-use traits alter intraspecific population yields. In the field and glasshouse, we observed overyielding in populations with low percentages of irMPK4 plants, unrelated to water-use phenotypes. Paired-plant experiments excluded the occurrence of overyielding effects at the neighbor scale. Experimentally altering field arbuscular mycorrhizal fungal associations by silencing the Sym-pathway gene NaCCaMK did not affect reproductive overyielding, implicating an effect independent of belowground AMF interactions. Additionally, micro-grafting experiments revealed dependence on shoot-expressed MPK4 for N. attenuata to vary its yield per neighbor presence. We find that variation in a single gene, MPK4, is responsible for population overyielding through a mechanism, independent of irMPK4's WUE phenotype, at the aboveground, population scale.

Whether on farmland or in a forest, plants do not grow in isolation. Plants compete with their neighbors over limited space and resources, and individual plants respond to this competition in different ways by changing how much they grow and how they use resources. The efficiency with which crop plants use water, for example, is one trait that is dramatically influenced by neighboring plants and is of increasing concern given the warming climate. Understanding the effects of interactions between individual plants in a population as a whole is complicated, especially in natural plant communities where neighbors are often from different species. For this reason, McGale et al. took a different approach and looked at neighbors that were all from the same species and differed only in the activity of a single gene. The species in question was coyote tobacco, a plant that is native to western North America. McGale et al. used genetic engineering to silence a gene called MPK4, which was known from previous studies to have the effect of reducing water-use efficiency. Some of these 'water-inefficient' plants were then grown in mixed populations with plants that had normal levels of MPK4. In experiments conducted both in a glasshouse and at a field station in the Utah desert, McGale et al. found that populations with a low percentage of the MPK4-silenced plants were actually more productive than 'monocultures' that were all one type or the other. Further analysis showed that the increase in productivity did not depend on the different soil nutrient or water use of the different populations, or even the density of the plants in the populations. Pairs of plants grown in single pots essentially ruled out any interactions between immediate neighbors being responsible for the increased productivity, suggesting that that effect must instead emerge at the level of the population. Perhaps unexpectedly, McGale et al. also found that the MPK4-silenced plants and control plants did not actually differ in how they used water when grown in the field (previous studies had all been conducted in glasshouses), indicating that this trait also could not explain the observed population-level effect. Finally, experiments that involved grafting the shoots of one plant onto the roots of another suggested that the effect most likely comes from the aboveground parts of the plant. Ecologists have previously noted that more diverse populations typically have higher productivity. This new finding that a small percentage of slightly different plants in an otherwise uniform population can increase overall productivity will likely to be of special interest to researchers looking to boost the efficiency of agricultural ecosystems. Also, since MPK4 is highly conserved, and thus likely to be found in many plant species, this could be an interesting trait with which to study the interactions of natural plant communities.

Bacterial community and nitrogen fixation in the red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae).

The red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae), colonizes all pines species within its native range throughout North and Central America. Recently, this species was accidentally introduced to China, where it has caused severe damage in pine forests. It belongs to a group of beetles that spend most of their lives between the tree bark and sapwood, where it feeds on phloem: a poor substrate with very low nutritional value of nitrogen and toxic properties due to its high content of secondary defensive compounds. The aim of this study was to characterize the bacterial community of the D. valens gut by culture-dependent and -independent methods. Polymerase chain reaction denaturing gradient gel electrophoresis and ribosomal gene library analyses revealed that species diversity in the D. valens gut was relatively low, containing between six and 17 bacterial species. The bacterial community associated with larvae and adults was dominated by members of the following genera: Lactococcus, Acinetobacter, Pantoea, Rahnella, Stenothrophomonas, Erwinia, Enterobacter, Serratia, Janibacter, Leifsonia, Cellulomonas, and Cellulosimicrobium. The members of the last four genera showed cellulolytic activity in vitro and could be involved in cellulose breakdown in the insect gut. Finally, nitrogen fixation was demonstrated in live larvae and adults; however, capacity of nitrogen fixing in vitro was not found among enterobacterial species isolated in nitrogen-free media; neither were nifD nor nifH genes detected. In contrast, nifD gen was detected in metagenomic DNA from insect guts. The identification of bacterial species and their potential physiological capacities will allow exploring the role of gut symbiotic bacteria in the adaptation and survival of D. valens in a harsh chemical habitat poor in nitrogen sources.

Cuautepestalorin, a 7,8-Dihydrochromene-Oxoisochromane Adduct Bearing a Hexacyclic Scaffold from Pestalotiopsis sp. IQ-011.

Cuautepestalorin (4), a 7,8-dihydrochromene-oxoisochromane adduct bearing a spiro-polycyclic (6/6/6/6/6/6) ring system, along with its putative biosynthetic precursors, cytosporin M (1), cytosporin N (2), and oxopestalochromane (3), were isolated from the bioactive extract of Pestalotiopsis sp. using a combination of molecular networking and dereplication techniques. Their structures were elucidated using a set of spectroscopic, spectrometric, chiroptical (experimental and theoretical), and X-ray crystallography data. Compounds 3 and 4 exhibited modest potency when evaluated in vitro as α-glucosidase inhibitors.

Modulation of tolerance to Cr(VI) and Cr(VI) reduction by sulfate ion in a Candida yeast strain isolated from tannery wastewater.

The main aim of this study was to investigate the influence of the sulfate ion on the tolerance to Cr(VI) and the Cr(VI) reduction in a yeast strain isolated from tannery wastewater and identified as Candida sp. FGSFEP by the D1/D2 domain sequence of the 26S rRNA gene. The Candida sp. FGSFEP strain was grown in culture media with sulfate concentrations ranging from 0 to 23.92 mM, in absence and presence of Cr(VI) [1.7 and 3.3 mM]. In absence of Cr(VI), the yeast specific growth rate was practically the same in every sulfate concentration tested, which suggests that sulfate had no stimulating or inhibiting effect on the yeast cell growth. In contrast, at the two initial Cr(VI) concentrations assayed, the specific growth rate of Candida sp. FGSFEP rose when sulfate concentration increased. Likewise, the greater efficiencies and volumetric rates of Cr(VI) reduction exhibited by Candida sp. FGSFEP were obtained at high sulfate concentrations. Yeast was capable of reducing 100% of 1.7 mM Cr(VI) and 84% of 3.3 mM Cr(VI), with rates of 0.98 and 0.44 mg Cr(VI)/L h, with 10 and 23.92 mM sulfate concentrations, respectively. These results indicate that sulfate plays an important role in the tolerance to Cr(VI) and Cr(VI) reduction in Candida sp. FGSFEP. These findings may have significant implications in the biological treatment of Cr(VI)-laden wastewaters.