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Activity cliffs: facts or artifacts?

José L Medina-Franco1

  • 1Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, Mexico. jose.medina.franco@gmail.com

Chemical Biology & Drug Design
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This summary is machine-generated.

Activity cliffs, sudden changes in compound activity, are crucial in drug discovery. This study questions whether detected cliffs are real or artifacts of computational methods and molecular representations.

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Area of Science:

  • Chemistry
  • Medicinal Chemistry
  • Computational Chemistry

Background:

  • Similar compounds can exhibit vastly different properties, impacting drug discovery.
  • Activity cliffs, sharp increases in compound activity with minor structural changes, are frequently encountered during lead optimization.

Purpose of the Study:

  • To critically evaluate the nature of activity cliffs in computational chemistry.
  • To discuss factors that may lead to the identification of false positive cliffs.

Main Methods:

  • Review and synthesis of existing computational approaches for detecting activity cliffs.
  • Analysis of potential artifacts in cliff identification, including molecular representation and similarity definitions.

Main Results:

  • Activity cliffs are a real phenomenon but their detection requires careful consideration.
  • Computational artifacts, such as inaccurate activity data or inappropriate molecular representations, can lead to false positive cliffs.

Conclusions:

  • The identification and quantification of activity cliffs must be approached with caution.
  • Distinguishing true activity cliffs from artifacts is essential for reliable structure-activity relationship (SAR) prediction in drug discovery.