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Cheminformatics Explorations of Natural Products

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Progress in the Chemistry of Organic Natural Products 110

Part of the book series: Progress in the Chemistry of Organic Natural Products ((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.

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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

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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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Authors and Affiliations

  1. Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico

    Fernando D. Prieto-Martínez & José L. Medina-Franco

  2. Department of Computer and Systems Sciences, Stockholm University, Kista, Sweden

    Ulf Norinder

  3. Unit of Toxicology Sciences, Swetox, Karolinska Institutet, Södertälje, Sweden

    Ulf Norinder

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  1. Fernando D. Prieto-Martínez
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  2. Ulf Norinder
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  3. José L. Medina-Franco
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Correspondence to José L. Medina-Franco .

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Editors and Affiliations

  1. College of Pharmacy, The Ohio State University, Columbus, OH, USA

    A. Douglas Kinghorn

  2. Institute of Organic Chemistry, Johannes Kepler University, Linz, Austria

    Heinz Falk

  3. UCL School of Pharmacy, University College London, Research, London, UK

    Simon Gibbons

  4. Grad. School of Pharmaceutical Science, Hokkaido University, Fukuoka, Japan

    Jun'ichi Kobayashi

  5. Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan

    Yoshinori Asakawa

  6. School of Pharmaceutical Sciences, South-Central Univ. for Nationalities, Wuhan, China

    Ji-Kai Liu

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Prieto-Martínez, F.D., Norinder, U., Medina-Franco, J.L. (2019). Cheminformatics Explorations of Natural Products. In: Kinghorn, A., Falk, H., Gibbons, S., Kobayashi, J., Asakawa, Y., Liu, JK. (eds) Progress in the Chemistry of Organic Natural Products 110. Progress in the Chemistry of Organic Natural Products, vol 110. Springer, Cham. https://doi.org/10.1007/978-3-030-14632-0_1

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