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Chemoinformatics-based enumeration of chemical libraries: a tutorial.

Fernanda I Saldívar-González1, C Sebastian Huerta-García2, José L Medina-Franco3

  • 1DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510, Mexico, Mexico. fer.saldivarg@gmail.com.

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|December 29, 2020
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Summary

This tutorial explores virtual compound library design for computer-assisted drug discovery. It details methods for enumerating chemical libraries using open-source tools and accessible reagents, aiding both beginners and experts.

Keywords:
Chemical enumerationChemoinformaticsCombinatorial librariesDOS synthesisDrug designEducationKNIMEPython

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Area of Science:

  • Computational chemistry
  • Medicinal chemistry
  • Chemoinformatics

Background:

  • Virtual compound libraries are crucial in computer-assisted drug discovery.
  • Numerous successful drug discovery cases have utilized virtual libraries.
  • Chemoinformatics tools facilitate the design and enumeration of these libraries.

Purpose of the Study:

  • To examine fundamental concepts of virtual library design.
  • To describe the enumeration of virtual libraries using open-source tools.
  • To provide a step-by-step tutorial for building chemical libraries.

Main Methods:

  • Emphasis on pre-validated reactions and accessible chemical reagents for library enumeration.
  • Utilizing open-access chemoinformatics tools to explore chemical space.
  • Demonstrating methodologies from synthetic organic chemistry.

Main Results:

  • Detailed tutorial on designing and building chemical libraries.
  • Exploration of affordable chemical space.
  • Three design examples: Diversity-Oriented-Synthesis (DOS) lactam library, bis-heterocyclic combinatorial library, and target-oriented isoindolinone compounds.

Conclusions:

  • The manuscript serves as a practical guide for chemoinformatics education and learning.
  • Empowers users with or without prior experience to design and build virtual chemical libraries.
  • Highlights the utility of open-source tools in modern drug discovery efforts.