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Cheminformatics Explorations of Natural Products

  • Fernando D. Prieto-Martínez
  • Ulf Norinder
  • José L. Medina-FrancoEmail author
Chapter
Part of the Progress in the Chemistry of Organic Natural Products book series (POGRCHEM, volume 110)

Abstract

The chemistry of natural products is fascinating and has continuously attracted the attention of the scientific community for many reasons including, but not limited to, biosynthesis pathways, chemical diversity, the source of bioactive compounds and their marked impact on drug discovery. There is a broad range of experimental and computational techniques (molecular modeling and cheminformatics) that have evolved over the years and have assisted the investigation of natural products. Herein, we discuss cheminformatics strategies to explore the chemistry and applications of natural products. Since the potential synergisms between cheminformatics and natural products are vast, we will focus on three major aspects: (1) exploration of the chemical space of natural products to identify bioactive compounds, with emphasis on drug discovery; (2) assessment of the toxicity profile of natural products; and (3) diversity analysis of natural product collections and the design of chemical collections inspired by natural sources.

Keywords

Chemical space Databases Epi-pharmacology Machine learning Target fishing Toxicity Virtual screening 

Abbreviations

BRD

Bromodomain

CDPs

Consensus Diversity Plots

DNMT

DNA methyltransferase

FDA

Food and Drug Administration

HDAC

Histone deacetylase

hERG

Human ether-a-go-go-related gene ion-channel

IMPS

Invalid metabolic panaceas

MACCS

Molecular Access System

PAINS

Pan-Assay Interference compounds

PCA

Principal component analysis

SAH

S-adenosyl homocysteine

SAM

S-adenosyl methionine

SMILES

Simplified Molecular Input Line Entries

TCM

Traditional Chinese Medicine

UNPD

Universal Natural Products Database

Notes

Acknowledgments

Fernando Prieto-Martínez is grateful for a Ph.D. scholarship from the Consejo Nacional de Ciencia y Tecnología (CONACyT) No. 660465/576637. The authors also thank the Programa de Nuevas Alternativas de Tratamiento para Enfermedades Infecciosas (NUATEI-IIB-UNAM). José Medina-Franco acknowledges the School of Chemistry of the Universidad Nacional Autónoma de México (UNAM), the Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT) grant number IA203718, UNAM and the Consejo Nacional de Ciencia y Tecnología grant number 282785. Fernando Prieto-Martínez and José Medina-Franco also thank Dirección General de Cómputo y de Tecnologías de Información y Comunicación (DGTIC), project grant LANCAD-UNAM-DGTIC-335 for the computational resources to use Miztli supercomputer at UNAM. The authors thank Fernanda I. Saldívar-González for providing the datasets on natural products used to compute the toxicity profile, Dr. Sharon Luna for assisting in the analysis of the toxicity data, and Edgar López-López for helpful discussions.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Fernando D. Prieto-Martínez
    • 1
  • Ulf Norinder
    • 2
    • 3
  • José L. Medina-Franco
    • 1
    Email author
  1. 1.Department of PharmacySchool of Chemistry, National Autonomous University of MexicoMexico CityMexico
  2. 2.Department of Computer and Systems SciencesStockholm UniversityKistaSweden
  3. 3.Unit of Toxicology SciencesSwetox, Karolinska InstitutetSödertäljeSweden

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