NPDBEjeCol: a natural products database from Colombia

The analysis of chemical data sets represents a significant challenge for researchers due to the large quantity and dispersion of the data. In order to facilitate accessible recovery, it is necessary to organize the data into databases. The aim of this research is to compile and analyze information on natural products derived from plants in the Coffee region of Colombia through the online Natural Products DataBase EjeCol (NPDBEjeCol). It is the first database of its kind for the country. The workflow for the creation of the database began with the compilation of reported molecules of natural products derived from plants studied and present to the Coffee region of Colombia. This was achieved through a systematic literature review and dataset compilation conducted using the specified bibliometric equations, with a focus on articles published up to December 2023 and collecting information from research groups at Colombian universities. Once the set of molecules had been curated, molecular descriptors and fingerprints were calculated in order to evaluate the structural diversity and explore their chemical space in comparison with natural products reference libraries. The NPDBEjeCol database contains 236 molecules, for which detailed information is available. This includes the compound name, SMILES notation, references (journal name, DOI number, and year of publication), CAS number, synonym names, and constitutional descriptors. The database places an emphasis on small molecules with an average molecular weight of 234.77 g/mol and features a high structural diversity. The calculated physicochemical properties are in accordance with Lipinski's Rule of Five. Visualizations using PCA and t-SNE demonstrate the existence of distinct clusters of compounds and fragments, thereby highlighting the structural diversity. The compound database is publicly accessible via the web portal www.npdbejecol.com. The objective of the website is to facilitate open consultation, navigation, management, and visualization of the molecules identified through research on natural products derived from plants in the coffee region of Colombia.