NPDBEjeCol: A Natural Products Database from Colombia

Abstract

The aim of this research is to introduce the first curated natural product database from Colombia, Natural Products DataBase EjeCol (NPDBEjeCol), that has been made publicly available at www.npdbejecol.com. The compound library, compiled from the peer-reviewed literature, is composed of natural products derived from plants in the coffee region of Colombia. After extensive data standardization and curation, molecular descriptors of pharmaceutical relevance and molecular fingerprints of different designs were calculated in order to evaluate the structural diversity and explore their chemical space of compounds in NPDBEjeCol in comparison with natural products reference libraries. The current version of NPDBEjeCol contains 236 molecules, for which detailed information is available. This includes the compound name, linear notation, references to the peer-reviewed literature, CAS number, synonym names, and constitutional descriptors. Analysis of the drug-like properties suggest that NPDBEjeCol natural products are on average, compliant with the empirical Lipinski’s rule. Visualizations of the chemical space based on fingerprints uncovered one to three clusters of compounds and fragments. Among the phytochemical groups present in the database, terpenes are the most prominent, particularly those derived from monoterpenes and sesquiterpenes. NPDBEjeCol is the first Colombian natural products database of its kind in the country that can be publicly accessed through a web portal, facilitating open query, navigation, and visualization of the identified molecules.