NP 3 MS Workflow: An Open-Source Software System to Empower Natural Product-Based Drug Discovery Using Untargeted Metabolomics.

Autor: Bazzano CF; 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., de Felicio R; Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil., Alves LFG; Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil., Costa JH; Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil., Ortega R; 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., Vieira BD; Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil., Morais-Urano RP; Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil., Furtado LC; Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, State of São Paulo, Brazil., Ferreira ELF; Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil., Gubiani JR; Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil., Berlinck RGS; Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos CEP 13560-970, State of São Paulo, Brazil., Costa-Lotufo LV; Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, State of São Paulo, Brazil., Telles GP; Institute of Computing, University of Campinas (UNICAMP), Campinas 13083-852, State of São Paulo, Brazil., B B Trivella D; Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, State of São Paulo, Brazil.
Jazyk: angličtina
Zdroj: Analytical chemistry [Anal Chem] 2024 May 14; Vol. 96 (19), pp. 7460-7469. Date of Electronic Publication: 2024 May 03.
DOI: 10.1021/acs.analchem.3c05829
Abstrakt: 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 NP 3 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. NP 3 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. NP 3 MS Workflow adds improved computing of the MS 2 spectra in an LC-MS/MS data set and provides tools for automatic [M + H] + ion deconvolution using fragmentation rules; chemical structural annotation against MS 2 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. NP 3 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.
Databáze: MEDLINE
Externí odkaz: