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Cheminformatics Approaches to Study Drug Polypharmacology

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Multi-Target Drug Design Using Chem-Bioinformatic Approaches

Part of the book series: Methods in Pharmacology and Toxicology ((MIPT))

Abstract

Herein is presented a tutorial overview on selected chemoinformatics methods useful for assembling, curating/preparing a chemical database, and assessing its diversity and chemical space. Methods for evaluating the structure–activity relationships (SAR) and polypharmacology are also included. Usage of open source tools is emphasized. Step-by-step KNIME workflows are used for illustrating the methods. The methods described in this chapter are applied onto a chemical database especially relevant for epi-polypharmacology that is an emerging area in drug discovery. However, the methods described herein could be extended to other therapeutic areas and potentially to other areas of chemistry.

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Acknowledgements

This work was supported by the Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT) grant IA203718 and National Council of Science and Technology (CONACyT), Mexico grant number 282785. JJN, FIS-G, and NS-C are thankful to CONACyT for the granted scholarships number 622969, 629458, and 335997, respectively.

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Authors and Affiliations

  1. Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico

    J. Jesús Naveja, Fernanda I. Saldívar-González, Norberto Sánchez-Cruz & José L. Medina-Franco

  2. PECEM, School of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico

    J. Jesús Naveja

Authors
  1. J. Jesús Naveja
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  2. Fernanda I. Saldívar-González
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  3. Norberto Sánchez-Cruz
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  4. José L. Medina-Franco
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Corresponding author

Correspondence to José L. Medina-Franco .

Editor information

Editors and Affiliations

  1. Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India

    Kunal Roy

Additional information

This work is dedicated to the loving memory of Nicolás Medina Sandoval.

1 Electronic Supplementary Material

The following supplementary KNIME files with exemplary workflows are provided:

Supplementary KNIME Workflow 1

Chemical preprocessing and database curation (KNWF 168 kb)

Supplementary KNIME Workflow 2

Chemical diversity analysis (KNWF 92 kb)

Supplementary KNIME Workflow 3

Consensus diversity plots (KNWF 127 kb)

Supplementary KNIME Workflow 4

SmARt analyses (KNWF 211 kb)

Supplementary KNIME Workflow 5

Chemical space (KNWF 399 kb)

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Naveja, J.J., Saldívar-González, F.I., Sánchez-Cruz, N., Medina-Franco, J.L. (2018). Cheminformatics Approaches to Study Drug Polypharmacology. In: Roy, K. (eds) Multi-Target Drug Design Using Chem-Bioinformatic Approaches. Methods in Pharmacology and Toxicology. Humana Press, New York, NY. https://doi.org/10.1007/7653_2018_6

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  • DOI: https://doi.org/10.1007/7653_2018_6

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  • Print ISBN: 978-1-4939-8732-0

  • Online ISBN: 978-1-4939-8733-7

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