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.

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.

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 (hPTP1B_1-282, hPTP1B_1-298, or hPTP1B_1-321), losing valuable information about the ligands' mechanism of inhibition and selectivity. Nevertheless, finding an allosteric site in hPTP1B_1-321, and the full-length (hPTP1B_1-400) 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 hPTP1B_1-400 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 hPTP1B_1-400 (IC₅₀ value of 8.8 ± 1.0 µM) in a mixed type fashion, with k_i and αk_i values of 5.5  and 6.6 μM, respectively. Docking xanthoepocin (1) with a homologated model of hPTP1B_1-400 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 hPTP1B_1-400 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 hPTP1B_1-400 (K_SV = 1.1 × 10⁵ M^-1), and corroborated that it binds to the enzyme with an affinity constant (k_a) of 3.7 × 10⁵ M^-1. Finally, the drug-likeness and medicinal chemistry friendliness of 1 were predicted with SwissADME.

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.

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.

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.

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.

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.

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.