Daniela B. B. Trivella^*

daniela.trivella@lnbio.cnpem.br

Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in energy and Material (CNPEM), 13083-100, Campinas, SP – Brazil.

In this talk the Drug Discovery platform in operation at CNPEM will be presented, along with the open access methods developed by the team. A special focus will be given to the Bank of Molecules collaborative program, the software “NP³ MS workflow”¹² and the “NP³ ligand”³ package. The Bank of Molecules is an open collaborative Program aimed to empower Brazilian natural product bioprospection, with activities done in synchrony at CNPEM and at partner laboratories. All academic groups are invited to be part of this Program. The “NP³ MS workflow” in an open access software used to accelerate bioprospection, enhancing molecular mapping using untargeted metabolomics and data analytics approaches. The NP³ ligands open package consists of a chemically labeled database (LigPCDS⁴⁵) of protein ligands and a software application (NP³ BlobLabel⁶) that work on trained deep learning models, based on LigPCDS, to decipher chemical structures – even of previously unknown molecules. The “NP³ ligand” package is based on protein crystallography data and can be used at different stages of bioprospection, starting from directly capturing of bioactive compounds from natural product mixtures, further revealing the binding sites of these molecules in their pharmacological targets.

Keywords: natural product bioprospection, LC-MS/MS untargeted metabolomics, high throughput protein crystallography, deep learning, drug discovery and development.

References:

1. Bazzano, C. F. et al. NP 3 MS Workflow: An Open-Source Software System to Empower Natural Product-Based Drug Discovery Using Untargeted Metabolomics. Anal. Chem. 96, 7460–7469 (2024) DOI: 10.1021/acs.analchem.3c05829.
2. Bazzano, C. F., Alves, L. F. G., de Felício, R., Telles, G. P. & Trivella, D. B. B. NP3 MS workflow INPI BR. 51 2021 000074-9. at https://github.com/danielatrivella/NP3_MS_Workflow (2020).
3. Bazzano, C. F., Alves, L. G., Telles, G. P. & Trivella, D. B. B. NP3 Ligand. NP3 Ligand https://github.com/danielatrivella/np3_ligand/.
4. Bazzano, C. F., Alves, L. F. G., Telles, G. P. & Trivella, D. B. B. LigPCDS: Labeled Dataset of X-ray Protein Ligand 3D Images in Point Clouds and Validated Deep Learning Models (1.0.0) [Data set]. Zenodo (2023) doi:10.5281/zenodo.7872577 DOI: 10.5281/zenodo.7872577.
5. Bazzano, C. F., Alves, L. G., Telles, G. P. & Trivella, D. B. B. Labeled dataset of X-ray protein ligand images in 3D point cloud and validated deep learning models. Sci. Data.
6. Bazzano, C. F., Alves, L. F. G., Rustiguel, J. K., Telles, G. P. & Trivella, D. B. B. NP3 Blob Label INPI BR.51 2023 001444-3. at (2023).

 
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