Functional group and diversity analysis of BIOFACQUIM: A Mexican natural product database

F1000Res. 2019 Dec 10:8:Chem Inf Sci-2071. doi: 10.12688/f1000research.21540.2. eCollection 2019.

Abstract

Background: Natural product databases are important in drug discovery and other research areas. An analysis of its structural content, as well as functional group occurrence, provides a useful overview, as well as a means of comparison with related databases. 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 performed. This involved a functional group analysis with a novel algorithm to automatically identify 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 15.7% of compounds and 11.6% of scaffolds 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 and scaffolds 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.

Keywords: Consensus Diversity Plot; compound databases; data mining; diversity; functional groups; in silico; natural products.

MeSH terms

  • Biological Products*
  • Databases, Chemical*
  • Drug Discovery
  • Mexico

Substances

  • Biological Products

Associated data

  • figshare/10.6084/m9.figshare.11312702

Grants and funding

This work was supported by a Consejo Nacional de Tecnología (CONACyT) scholarship number 335997 (NS-C). The work was also supported by the program NUATEI (Nuevas Alternativas para el Tratamiento de Enfermedades Infecciosas), Instituto de Ciencias Biomédicas, UNAM. The authors are grateful for the computational resources granted by Dirección General de Cómputo y de Tecnologías de Información y Comunicación (DGTIC), project grant LANCAD-UNAM-DGTIC-335 that allows to use the supercomputer Miztli at UNAM.