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Cheminformatics Approaches to Study Drug Polypharmacology

  • J. Jesús Naveja
  • Fernanda I. Saldívar-González
  • Norberto Sánchez-Cruz
  • José L. Medina-FrancoEmail author
Protocol
Part of the Methods in Pharmacology and Toxicology book series (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.

Keywords

Chemoinformatics ChemMaps Chemical space Data mining Epigenetics Epi-informatics KNIME Molecular diversity Open-access Polypharmacology Structure–activity relationships SmARt 

Notes

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.

Supplementary material

457674_1_En_6_MOESM1_ESM.knwf (169 kb)
Supplementary KNIME Workflow 1 Chemical preprocessing and database curation (KNWF 168 kb)
457674_1_En_6_MOESM2_ESM.knwf (93 kb)
Supplementary KNIME Workflow 2 Chemical diversity analysis (KNWF 92 kb)
457674_1_En_6_MOESM3_ESM.knwf (128 kb)
Supplementary KNIME Workflow 3 Consensus diversity plots (KNWF 127 kb)
457674_1_En_6_MOESM4_ESM.knwf (212 kb)
Supplementary KNIME Workflow 4 SmARt analyses (KNWF 211 kb)
457674_1_En_6_MOESM5_ESM.knwf (400 kb)
Supplementary KNIME Workflow 5 Chemical space (KNWF 399 kb)

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Copyright information

© Springer Science+Business Media New York 2018

Authors and Affiliations

  • J. Jesús Naveja
    • 1
    • 2
  • Fernanda I. Saldívar-González
    • 1
  • Norberto Sánchez-Cruz
    • 1
  • José L. Medina-Franco
    • 1
    Email author
  1. 1.Department of Pharmacy, School of ChemistryUniversidad Nacional Autónoma de MéxicoMexico CityMexico
  2. 2.PECEM, School of MedicineUniversidad Nacional Autónoma de MéxicoMexico CityMexico

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