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An Automated, Open-Source Workflow for the Generation of (3D) Fragment Libraries.

Tom Dekker1, Mathilde A C H Janssen2, Christina Sutherland1

  • 1Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.

ACS Medicinal Chemistry Letters
|May 17, 2023
PubMed
Summary

Automated workflow design enhances fragment libraries for drug discovery. This tool ensures chemical diversity and novelty, improving screening compound selection for better drug development outcomes.

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Area of Science:

  • Medicinal Chemistry
  • Computational Chemistry
  • Drug Discovery

Background:

  • Fragment-based drug discovery (FBDD) success relies heavily on effective fragment library design.
  • Existing fragment libraries may lack diversity or novelty, impacting screening efficiency.

Purpose of the Study:

  • To develop an automated workflow for designing fragment libraries.
  • To incorporate chemical diversity, novelty, and three-dimensional (3D) characteristics into library design.
  • To enable the creation of both large, diverse libraries and focused, representative compound sets.

Main Methods:

  • Construction of an automated workflow using the open-source KNIME software.
  • Integration of parameters for chemical diversity, novelty, and 3D shape.
  • Design and synthesis of a 10-membered focused library based on a cyclopropane scaffold.

Main Results:

  • The workflow successfully generated a focused library with significant shape diversity.
  • The designed compounds exhibited a favorable physicochemical profile.
  • The modular workflow allows for customization to prioritize different properties.

Conclusions:

  • The automated workflow provides a powerful tool for rational fragment library design.
  • This approach can enrich existing fragment libraries with unique and diverse compounds.
  • The methodology is adaptable for designing libraries focused on various properties beyond 3D shape.