Abstract
Background: Natural product databases are important in drug discovery and other research areas. Their structural contents and functional group analysis are relevant to increase their knowledge in terms of chemical diversity and chemical space coverage. BIOFACQUIM is an emerging database of natural products characterized and isolated in Mexico. Herein, we discuss the results of a first systematic functional group analysis and global diversity of an updated version of BIOFACQUIM. Methods: BIOFACQUIM was augmented through a literature search and data curation. A structural content analysis of the dataset was done. This involved a functional group analysis with a novel algorithm to identify automatically all functional groups in a molecule and an assessment of the global diversity using consensus diversity plots. To this end, BIOFACQUIM was compared to two major and large databases: ChEMBL 25, and a herein assembled collection of natural products with 169,839 unique compounds. Results: The structural content analysis showed that 16.1% of compounds, 11.3% of scaffolds, and 6.3% of functional groups present in the current version of BIOFACQUIM have not been reported in the other large reference datasets. It also gave a diversity increase in terms of scaffolds and molecular fingerprints regarding the previous version of the dataset, as well as a higher similarity to the assembled collection of natural products than to ChEMBL 25, in terms of diversity and frequent functional groups. Conclusions: A total of 148 natural products were added to BIOFACQUIM, which meant a diversity increase in terms of scaffolds and fingerprints. Regardless of its relatively small size, there are a significant number of compounds, scaffolds, and functional groups that are not present in the reference datasets, showing that curated databases of natural products, such as BIOFACQUIM, can serve as a starting point to increase the biologically relevant chemical space.
Highlights
Natural product-based drug discovery continues to be an important part of drug discovery
Database overlap To assess the chemical space not covered by ChEMBL and natural products (NPs) but by BIOFACQUIM, we characterized the structural content of the three datasets in terms of unique compounds, scaffolds and functional groups and determined the overlap among them
It should be noted that despite its small size in comparison with ChEMBL and NPs, 16.1% of compounds present in BIOFACQUIM have not been reported in those other major datasets, as well as 11.3% of its scaffolds and 6.3% of its functional group (FG)
Summary
Natural product-based drug discovery continues to be an important part of drug discovery. Natural product databases are important in drug discovery and other research areas Their structural contents and functional group analysis are relevant to increase their knowledge in terms of chemical diversity and chemical space coverage. Results: The structural content analysis showed that 16.1% of compounds, 11.3% of scaffolds, and 6.3% of functional groups present in the current version of BIOFACQUIM have not been reported in the other large reference datasets It gave a diversity increase in terms of scaffolds and molecular fingerprints regarding the previous version of the dataset, as well as a higher similarity to the assembled collection of natural products than to ChEMBL 25, in terms of diversity and frequent functional groups. Regardless of its relatively small size, there are a significant number of compounds, scaffolds, and functional groups that are not present in the reference datasets, showing that curated databases of natural products, such as BIOFACQUIM, can serve as a starting point to increase the biologically relevant chemical space
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