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Navigating chemical reaction space - application to DNA-encoded chemistry.

Silvia Chines1, Christiane Ehrt2, Marco Potowski1

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Summary

Reaction Navigator, a computational workflow, aids in selecting chemical reactions for DNA-encoded libraries (DELs). It processes reaction data, filters incompatibilities, and clusters reactions for efficient library design.

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Area of Science:

  • Computational chemistry
  • Medicinal chemistry
  • Drug discovery

Background:

  • Selecting reactions for synthesizing small molecule screening libraries, like DNA-encoded libraries (DELs), is a significant big data challenge due to the vast number of available reactions.
  • Existing methods often struggle to efficiently navigate and select appropriate reactions compatible with DEL synthesis constraints, such as avoiding damage to the genetic barcode.

Purpose of the Study:

  • To develop a computational workflow, Reaction Navigator, for navigating chemical reaction space and facilitating the selection of suitable reactions for DNA-encoded library (DEL) synthesis.
  • To enable efficient identification of reactions based on user-defined criteria, independent of specific substitution patterns.

Main Methods:

  • Utilized the open-source KNIME Analytics Platform to process reaction files from a large chemistry database.
  • Implemented a customizable filtering cascade to remove reactions incompatible with DEL synthesis.
  • Developed a clustering approach based on user-defined molecular reaction descriptors to organize and search reaction space.

Main Results:

  • Successfully mapped chemical reaction space for aromatic aldehydes, identifying reactions applicable to DEL synthesis.
  • Demonstrated the successful translation of exemplary reactions to DNA-tagged substrates for library synthesis.
  • Showcased the workflow's versatility by mapping reaction space for amines and data from a second database, under various reaction conditions.

Conclusions:

  • Reaction Navigator provides an effective computational solution for navigating complex reaction spaces in the context of DNA-encoded library design.
  • The workflow enhances the efficiency and applicability of reaction selection for creating diverse and functional small molecule libraries.
  • The developed methodology is adaptable and can be applied to different starting materials, reaction conditions, and chemical databases.