NP3 MS Workflow: An Open-Source Software System to Empower Natural Product-Based Drug Discovery Using Untargeted Metabolomics.

Natural products (or specialized metabolites) are historically the main source of new drugs. However, the current drug discovery pipelines require miniaturization and speeds that are incompatible with traditional natural product research methods, especially in the early stages of the research. This article introduces the NP3 MS Workflow, a robust open-source software system for liquid chromatography-tandem mass spectrometry (LC-MS/MS) untargeted metabolomic data processing and analysis, designed to rank bioactive natural products directly from complex mixtures of compounds, such as bioactive biota samples. NP3 MS Workflow allows minimal user intervention as well as customization of each step of LC-MS/MS data processing, with diagnostic statistics to allow interpretation and optimization of LC-MS/MS data processing by the user. NP3 MS Workflow adds improved computing of the MS2 spectra in an LC-MS/MS data set and provides tools for automatic [M + H]+ ion deconvolution using fragmentation rules; chemical structural annotation against MS2 databases; and relative quantification of the precursor ions for bioactivity correlation scoring. The software will be presented with case studies and comparisons with equivalent tools currently available. NP3 MS Workflow shows a robust and useful approach to select bioactive natural products from complex mixtures, improving the set of tools available for untargeted metabolomics. It can be easily integrated into natural product-based drug-discovery pipelines and to other fields of research at the interface of chemistry and biology.

Production of Epoxyketone Peptide-Based Proteasome Inhibitors by Streptomyces sp. BRA-346: Regulation and Biosynthesis.

Streptomyces sp. BRA-346 is an Actinobacteria isolated from the Brazilian endemic tunicate Euherdmania sp. We have reported that this strain produces epoxyketone peptides, as dihydroeponemycin (DHE) and structurally related analogs. This cocktail of epoxyketone peptides inhibits the proteasome chymotrypsin-like activity and shows high cytotoxicity to glioma cells. However, low yields and poor reproducibility of epoxyketone peptides production by BRA-346 under laboratory cultivation have limited the isolation of epoxyketone peptides for additional studies. Here, we evaluated several cultivation methods using different culture media and chemical elicitors to increase the repertoire of peptide epoxyketone production by this bacterium. Furthermore, BRA-346 genome was sequenced, revealing its broad genetic potential, which is mostly hidden under laboratory conditions. By using specific growth conditions, we were able to evidence different classes of secondary metabolites produced by BRA-346. In addition, by combining genome mining with untargeted metabolomics, we could link the metabolites produced by BRA-346 to its genetic capacity and potential regulators. A single biosynthetic gene cluster (BGC) was related to the production of the target epoxyketone peptides by BRA-346. The candidate BGC displays conserved biosynthetic enzymes with the reported eponemycin (EPN) and TMC-86A (TMC) BGCs. The core of the putative epoxyketone peptide BGC (ORFs A-L), in which ORF A is a LuxR-like transcription factor, was cloned into a heterologous host. The recombinant organism was capable to produce TMC and EPN natural products, along with the biosynthetic intermediates DH-TMC and DHE, and additional congeners. A phylogenetic analysis of the epn/tmc BGC revealed related BGCs in public databases. Most of them carry a proteasome beta-subunit, however, lacking an assigned specialized metabolite. The retrieved BGCs also display a diversity of regulatory genes and TTA codons, indicating tight regulation of this BGC at the transcription and translational levels. These results demonstrate the plasticity of the epn/tmc BGC of BRA-346 in producing epoxyketone peptides and the feasibility of their production in a heterologous host. This work also highlights the capacity of BRA-346 to tightly regulate its secondary metabolism and shed light on how to awake silent gene clusters of Streptomyces sp. BRA-346 to allow the production of pharmacologically important biosynthetic products.

Cryo-EM structure of the mature and infective Mayaro virus at 4.4 Å resolution reveals features of arthritogenic alphaviruses.

Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related arthritogenic alphaviruses. Here, we present the structure of MAYV at 4.4 Å resolution, obtained from a preparation of mature, infective virions. MAYV presents typical alphavirus features and organization. Interactions between viral proteins that lead to particle formation are described together with a hydrophobic pocket formed between E1 and E2 spike proteins and conformational epitopes specific of MAYV. We also describe MAYV glycosylation residues in E1 and E2 that may affect MXRA8 host receptor binding, and a molecular "handshake" between MAYV spikes formed by N262 glycosylation in adjacent E2 proteins. The structure of MAYV is suggestive of structural and functional complexity among alphaviruses, which may be targeted for specificity or antiviral activity.

Chemical Elicitors Induce Rare Bioactive Secondary Metabolites in Deep-Sea Bacteria under Laboratory Conditions.

Bacterial genome sequencing has revealed a vast number of novel biosynthetic gene clusters (BGC) with potential to produce bioactive natural products. However, the biosynthesis of secondary metabolites by bacteria is often silenced under laboratory conditions, limiting the controlled expression of natural products. Here we describe an integrated methodology for the construction and screening of an elicited and pre-fractionated library of marine bacteria. In this pilot study, chemical elicitors were evaluated to mimic the natural environment and to induce the expression of cryptic BGCs in deep-sea bacteria. By integrating high-resolution untargeted metabolomics with cheminformatics analyses, it was possible to visualize, mine, identify and map the chemical and biological space of the elicited bacterial metabolites. The results show that elicited bacterial metabolites correspond to ~45% of the compounds produced under laboratory conditions. In addition, the elicited chemical space is novel (~70% of the elicited compounds) or concentrated in the chemical space of drugs. Fractionation of the crude extracts further evidenced minor compounds (~90% of the collection) and the detection of biological activity. This pilot work pinpoints strategies for constructing and evaluating chemically diverse bacterial natural product libraries towards the identification of novel bacterial metabolites in natural product-based drug discovery pipelines.

Carotenoids produced by the deep-sea bacterium Erythrobacter citreus LAMA 915: detection and proposal of their biosynthetic pathway.

Technologies based on synthetic biology to produce bacterial natural carotenoids depend on information regarding their biosynthesis. Although the biosynthetic pathway of common carotenoids is known, there are carotenoids whose pathways are not completely described. This work aimed to mine the genome of the deep-sea bacterium Erythrobacter citreus LAMA 915, an uncommon bacterium that forms yellow colonies under cultivation. This work further explores the potential application of the carotenoids found and low-cost substrates for bacterial growth. A combined approach of genome mining and untargeted metabolomics analysis was applied. The carotenoid erythroxanthin sulfate was detected in E. citreus LAMA 915 cell extract. A proposal for carotenoid biosynthesis by this bacterium is provided, involving the genes crtBIYZWG. These are responsible for the biosynthesis of carotenoids from the zeaxanthin pathway and their 2,2'-hydroxylated derivatives. E. citreus LAMA 915 extracts showed antioxidant and sun protection effects. Based on the high content of proteases and lipases, it was possible to rationally select substrates for bacterial growth, with residual oil from fish processing the best low-cost substrate selected. This work advances in the understanding of carotenoid biosynthesis and provides a genetic basis that can be further explored as a biotechnological route for carotenoid production.

Merulinic acid C overcomes gentamicin resistance in Enterococcus faecium.

Enterococci are gram-positive, widespread nosocomial pathogens that in recent years have developed resistance to various commonly employed antibiotics. Since finding new infection-control agents based on secondary metabolites from organisms has proved successful for decades, natural products are potentially useful sources of compounds with activity against enterococci. Herein are reported the results of a natural product library screening based on a whole-cell assay against a gram-positive model organism, which led to the isolation of a series of anacardic acids identified by analysis of their spectroscopic data and by chemical derivatizations. Merulinic acid C was identified as the most active anacardic acid derivative obtained against antibiotic-resistant enterococci. Fluorescence microscopy analyses showed that merulinic acid C targets the bacterial membrane without affecting the peptidoglycan and causes rapid cellular ATP leakage from cells. Merulinic acid C was shown to be synergistic with gentamicin against Enterococcus faecium, indicating that this compound could inspire the development of new antibiotic combinations effective against drug-resistant pathogens.

Structure-function relationship of a citrus salicylate methylesterase and role of salicylic acid in citrus canker resistance.

Salicylic acid (SA) and its methyl ester, methyl salicylate (MeSA) are well known inducers of local and systemic plant defense responses, respectively. MeSA is a major mediator of systemic acquired resistance (SAR) and its conversion back into SA is thought to be required for SAR. In many plant species, conversion of MeSA into SA is mediated by MeSA esterases of the SABP2 family. Here we show that the Citrus sinensis SABP2 homologue protein CsMES1 catalyzes the hydrolysis of MeSA into SA. Molecular modeling studies suggest that CsMES1 shares the same structure and SA-binding mode with tobacco SABP2. However, an amino acid polymorphism in the active site of CsMES1-related proteins suggested an important role in enzyme regulation. We present evidence that the side chain of this polymorphic residue directly influences enzyme activity and SA binding affinity in CsMES proteins. We also show that SA and CsMES1 transcripts preferentially accumulate during the incompatible interaction between Xanthomonas aurantifolii pathotype C and sweet orange plants. Moreover, we demonstrate that SA and MeSA inhibited citrus canker caused by Xanthomonas citri, whereas an inhibitor of CsMES1 enhanced canker formation, suggesting that CsMES1 and SA play a role in the local defense against citrus canker bacteria.

The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking.

Natural products are the richest source of chemical compounds for drug discovery. Particularly, bacterial secondary metabolites are in the spotlight due to advances in genome sequencing and mining, as well as for the potential of biosynthetic pathway manipulation to awake silent (cryptic) gene clusters under laboratory cultivation. Further progress in compound detection, such as the development of the tandem mass spectrometry (MS/MS) molecular networking approach, has contributed to the discovery of novel bacterial natural products. The latter can be applied directly to bacterial crude extracts for identifying and dereplicating known compounds, therefore assisting the prioritization of extracts containing novel natural products, for example. In our opinion, these three approaches-genome mining, silent pathway induction, and MS-based molecular networking-compose the tripod for modern bacterial natural product discovery and will be discussed in this perspective.

The azo dye Disperse Red 13 and its oxidation and reduction products showed mutagenic potential.

Common water pollutants, azo dyes and their degradation products have frequently shown toxicity, including carcinogenic and mutagenic effects, and can induce serious damage in aquatic organisms and humans. In the present study, the mutagenic potential of the azo dye Disperse Red 13 (DR13) was first evaluated using the Micronucleus Assay in human lymphocytes. Subsequently, in order to mimic hepatic biotransformation, controlled potential electrolysis was carried out with a DR13 solution using a Potentiostat/Galvanostat. In addition, a DR13 solution was oxidized using S9 (homogenate of rat liver cells). DR13 oxidation and the reduction products were identified using HPLC-DAD and GC/MS, and their mutagenic potential investigated by way of a Salmonella/microsome assay using TA98 and YG1041 strains, with no S9. The original azo dye DR13 induced chromosomal damage in human lymphocytes, and the respective oxidation and reduction products also showed mutagenic activity, as detected by the Salmonella/microsome assay. Furthermore sulfate 2-[(4-aminophenyl)ethylamino]-ethanol monohydrate, 2-chloro-4-nitro-benzamine, 4-nitro-benzamine and 2-(ethylphenylamine)-ethanol were identified as products of the DR13 reduction/oxidation reactions. Thus it was concluded that the contamination of water effluents with DR13 is a health risk not only due to the dye itself, but also due to the possibility of drinking contaminated water, considering the harmful compounds that can be produced after hepatic biotransformation.

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.

Analyses of the genotoxic and mutagenic potential of the products formed after the biotransformation of the azo dye Disperse Red 1.

Azo dyes constitute the largest class of synthetic dyes. Following oral exposure, these dyes can be reduced to aromatic amines by the intestinal microflora or liver enzymes. This work identified the products formed after oxidation and reduction of the dye Disperse Red 1, simulating hepatic biotransformation and evaluated the mutagenic potential of the resultant solution. Controlled potential electrolysis was carried out on dye solution using a Potentiostat/Galvanostat. HPLC-DAD and GC/MS were used to determine the products generated after the oxidation/reduction process. The Salmonella/microsome assay with the strains TA98 and YG1041 without S9, and the mouse lymphoma assay (MLA) using the thymidine kinase (Tk) gene, were used to evaluate the mutagenicity of the products formed. Sulfate 2-[(4-aminophenyl)ethylamino]-ethanol monohydrate, nitrobenzene, 4-nitro-benzamine and 2-(ethylphenylamino)-ethanol were detected. This dye has already being assigned as mutagenic in different cell system. In addition, after the oxidation/reduction process the dye still had mutagenic activity for the Salmonella/microsome assay. Nevertheless, both the original dye Disperse Red 1 and its treated solutions showed negative results in the MLA. The present results suggest that the ingestion of water and food contaminated with this dye may represent human and environmental health problem, due to the generation of harmful compounds after biotransformation.

Chemical profile and biological potential of non-polar fractions from Centroceras clavulatum (C. Agardh) Montagne (Ceramiales, Rhodophyta).

The present study reports the Gas Chromatography-Mass Spectrometry (GC-MS) evaluation of the hexanes and dichloromethane fractions from extracts of the red alga Centroceras clavulatum (C. Agardh) Montagne. Twenty three compounds were identified, totaling ca. 42% of both fractions (0.18 g mass extract). The main constituents of the fractions were hexadecanoic acid (17.6%) and pentadecanoic acid (15.9%). Several secondary metabolites with interesting biological activity, such as (-)-loliolide, neophytadiene, phytol were identified. In addition, several classes of secondary metabolites, including phenolic compounds (e.g., phenylacetic acid), terpene derivatives, fatty acids, halogenated compound (e.g., 2-chlorocyclohexenol), lignoids, steroids, esters, amides (e.g., hexadecanamide), ketones, carboxylic acids, aldehydes and alcohols were observed. The occurrence of several of these structural classes is described for the first time in this species. The same fractions analyzed by GC-MS, and a separate set of polar fractions, were evaluated against two life cycle stages (epimastigote and trypomastigote forms) of the protozoan Trypanosoma cruzi and against phytopatogenic fungi Cladosporium cladosporiodes and C. sphaerospermum. The dichloromethane fraction was active against both T. cruzi forms (epimastigote IC(50) = 19.1 µg.mL-1 and trypomastigote IC(50) = 76.2 µg.mL-1). The hexanes and ethyl acetate fractions also displayed activity against both fungi species (200 µg) by TLC-bioautography.

Trypanocidal, leishmanicidal and antifungal potential from marine red alga Bostrychia tenella J. Agardh (Rhodomelaceae, Ceramiales).

Specimens of the red alga Bostrychia tenella J. Agardh (Rhodomelaceae, Ceramiales) were collected from the São Paulo coast and submitted to room temperature solvent extraction. The resulting extract was fractionated by partitioning with organic solvent. The n-hexane (BT-H) and dichloromethane (BT-D) fractions showed antiprotozoal potential in biological tests with Trypanosoma cruzi and Leishmania amazonensis and presented high activity in an antifungal assay with the phytopathogenic fungi Cladosporium cladosporioides and Cladosporium sphaerospermum. Chromatography methods were used to generate subfractions from BT-H (H01 to H11) and from BT-D (D01 to D19). The subfractions were analyzed by gas chromatography-mass spectrometry (GC/MS), and the substances were identified by retention index (Kovats) and by comparison to databases of commercial mass spectra. The volatile compounds found in marine algae were identified as fatty acids, low molecular mass hydrocarbons, esters and steroids; some of these have been previously described in the literature based on other biological activities. Moreover, uncommon substances, such as neophytadiene were also identified. In a trypanocidal assay, fractions BT-H and BT-D showed IC(50) values of 16.8 and 19.1 microg/mL, respectively, and were more active than the gentian violet standard (31 microg/mL); subfractions H02, H03, D01 and D02 were active against L. amasonensis, exhibiting IC(50) values of 1.5, 2.7, 4.4, and 4.3 microg/mL, respectively (standard amphotericin B: IC(50)=13 microg/mL). All fractions showed antifungal potential. This work reports the biological activity and identification of compounds by GC/MS for the marine red alga B. tenella for the first time.