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Bazzano CF, de Felicio R, Alves LFG, Costa JH, Ortega R, Vieira BD, Morais-Urano RP, Furtado LC, Ferreira ELF, Gubiani JR, Berlinck RGS, Costa-Lotufo LV, Telles GP, B B Trivella D. NP 3 MS Workflow: An Open-Source Software System to Empower Natural Product-Based Drug Discovery Using Untargeted Metabolomics. Anal Chem 2024. [PMID: 38702053 DOI: 10.1021/acs.analchem.3c05829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
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.
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Affiliation(s)
- Cristina F Bazzano
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil
- Institute of Computing, University of Campinas (UNICAMP), Campinas 13083-852, State of São Paulo, Brazil
| | - Rafael de Felicio
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil
| | - Luiz Fernando Giolo Alves
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil
| | - Jonas Henrique Costa
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil
| | - Raquel Ortega
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil
- Institute of Biology, University of Campinas (UNICAMP), Campinas 13083-852, State of São Paulo, Brazil
| | - Bruna Domingues Vieira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil
| | - Raquel Peres Morais-Urano
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil
| | - Luciana Costa Furtado
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, State of São Paulo, Brazil
| | - Everton L F Ferreira
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil
| | - Leticia V Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, State of São Paulo, Brazil
| | - Guilherme P Telles
- Institute of Computing, University of Campinas (UNICAMP), Campinas 13083-852, State of São Paulo, Brazil
| | - Daniela B B Trivella
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil
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Bauermeister A, Furtado LC, Ferreira EG, Moreira EA, Jimenez PC, Lopes NP, Araújo WL, Olchanheski LR, Monteiro da Cruz Lotufo T, Costa-Lotufo LV. Chemical and microbial diversity of a tropical intertidal ascidian holobiont. Mar Environ Res 2024; 194:106303. [PMID: 38150785 DOI: 10.1016/j.marenvres.2023.106303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023]
Abstract
The tropical ascidian Eudistoma vannamei, endemic to the northeastern coast of Brazil, is considered a prolific source of secondary metabolites and hosts Actinomycetota that produce bioactive compounds. Herein, we used an omics approach to study the ascidian as a holobiont, including the microbial diversity through 16S rRNA gene sequencing and metabolite production using mass spectrometry-based metabolomics. Gene sequencing analysis revealed all samples of E. vannamei shared about 50% of the observed ASVs, and Pseudomonadota (50.7%), Planctomycetota (9.58%), Actinomycetota (10.34%), Bacteroidota (12.05%) were the most abundant bacterial phyla. Analysis of tandem mass spectrometry (MS/MS) data allowed annotation of compounds, including phospholipids, amino acids, and pyrimidine alkaloids, such as staurosporine, a member of a well-known chemical class recognized as a microbial metabolite. Isolated bacteria, mainly belonging to Streptomyces and Micromonospora genera, were cultivated and extracted with ethyl acetate. MS/MS analysis of bacterial extracts allowed annotation of compounds not detected in the ascidian tissue, including marineosin and dihydroergotamine, yielding about 30% overlapped ions between host and isolated bacteria. This study reveals E. vannamei as a rich source of microbial and chemical diversity and, furthermore, highlights the importance of omic tools for a comprehensive investigation of holobiont systems.
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Affiliation(s)
- Anelize Bauermeister
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil; Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Luciana Costa Furtado
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Elthon G Ferreira
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, CE, 60451-970, Brazil
| | - Eduarda Antunes Moreira
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Norberto Peporine Lopes
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Welington Luiz Araújo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Luiz Ricardo Olchanheski
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | | | - Leticia Veras Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil.
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Domingues Vieira B, Niero H, de Felício R, Giolo Alves LF, Freitas Bazzano C, Sigrist R, Costa Furtado L, Felix Persinoti G, Veras Costa-Lotufo L, Barretto Barbosa Trivella D. Production of Epoxyketone Peptide-Based Proteasome Inhibitors by Streptomyces sp. BRA-346: Regulation and Biosynthesis. Front Microbiol 2022; 13:786008. [PMID: 35401454 PMCID: PMC8988807 DOI: 10.3389/fmicb.2022.786008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Bruna Domingues Vieira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Faculty of Pharmaceutical Sciences (FCF), University of Campinas (UNICAMP), Campinas, Brazil
| | - Henrique Niero
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Faculty of Pharmaceutical Sciences (FCF), University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael de Felício
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Luiz Fernando Giolo Alves
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Cristina Freitas Bazzano
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Institute of Computing (IC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Renata Sigrist
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Luciana Costa Furtado
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniela Barretto Barbosa Trivella
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- *Correspondence: Daniela Barretto Barbosa Trivella,
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Hirakata C, Lima K, De Almeida BO, De Miranda LBL, Florêncio KGD, Furtado LC, Costa-Lotufo LV, Machado-Neto JA. Targeting glioma cells by antineoplastic activity of reversine. Oncol Lett 2021; 22:610. [PMID: 34188712 PMCID: PMC8227489 DOI: 10.3892/ol.2021.12871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/02/2021] [Indexed: 12/30/2022] Open
Abstract
Gliomas are the most common type of primary central nervous system tumors and despite great advances in understanding the molecular basis of the disease very few new therapies have been developed. Reversine, a synthetic purine analog, is a multikinase inhibitor that targets aurora kinase A (AURKA) and aurora kinase B (AURKB). In gliomas, a high expression of AURKA or AURKB is associated with a malignant phenotype and a poor prognosis. The present study investigated reversine-related cellular and molecular antiglioma effects in HOG, T98G and U251MG cell lines. Gene and protein expression were assessed by reverse transcription-quantitative PCR and western blotting, respectively. For functional assays, human glioma cell lines (HOG, T98G and U251MG) were exposed to increasing concentrations of reversine (0.4–50 µM) and subjected to various cellular and molecular assays. Reversine reduced the viability and clonogenicity in a dose- and/or time-dependent manner in all glioma cells, with HOG (high AURKB-expression) and T98G (high AURKA-expression) cells being more sensitive compared with U251MG cells (low AURKA- and AURKB-expression). Notably, HOG cells presented higher levels of polyploidy, while T98G presented multiple mitotic spindles, which is consistent with the main regulatory functions of AURKB and AURKA, respectively. In molecular assays, reversine reduced AURKA and/or AURKB expression/activity and increased DNA damage and apoptosis markers, but autophagy-related proteins were not modulated. In conclusion, reversine potently induced mitotic catastrophe and apoptosis in glioma cells and higher basal levels of aurora kinases and genes responsive to DNA damage and may predict improved antiglioma responses to the drug. Reversine may be a potential novel drug in the antineoplastic arsenal against gliomas.
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Affiliation(s)
- Camila Hirakata
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-900, Brazil
| | - Keli Lima
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-900, Brazil
| | - Bruna Oliveira De Almeida
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-900, Brazil
| | - Lívia Bassani Lins De Miranda
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-900, Brazil
| | - Katharine Gurgel Dias Florêncio
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Luciana Costa Furtado
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-900, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-900, Brazil
| | - João Agostinho Machado-Neto
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-900, Brazil
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Bauermeister A, Branco PC, Furtado LC, Jimenez PC, Costa-Lotufo LV, da Cruz Lotufo TM. Tunicates: A model organism to investigate the effects of associated-microbiota on the production of pharmaceuticals. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ddmod.2019.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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