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Peptide-based Identification of Functional Motifs and their Binding Partners
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Published on: June 30, 2013

Exploring peptide-likeness of active molecules using 2D fingerprint methods.

Hanna Eckert1, Jürgen Bajorath

  • 1Department of Life Science Informatics, B-IT, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany.

Journal of Chemical Information and Modeling
|June 2, 2007
PubMed
Summary

This study explores 2D fingerprints for identifying peptide-like molecules with varying biological activities. Certain fingerprints effectively distinguish activity and track the transition from strong to weak peptide character, aiding drug discovery.

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Area of Science:

  • Medicinal Chemistry
  • Computational Chemistry
  • Drug Discovery

Background:

  • Similarity searching for peptide-like small molecules is challenging due to the amide backbone masking key activity-determining features.
  • Differentiating biological activity and guiding peptidomimetic transitions requires specialized search strategies.

Purpose of the Study:

  • To evaluate the efficacy of 2D fingerprints in distinguishing peptide-like molecules with different biological activities.
  • To assess the ability of 2D fingerprints to facilitate the transition from peptide-like compounds to non-peptide-like ones.
  • To introduce and utilize a "peptide flavor" index for quantifying peptide character.

Main Methods:

  • Assembly of compound activity classes with varying degrees of peptide character (strong, moderate, weak).
  • Introduction and application of a "peptide flavor" index for quantitative assessment of peptide character.
  • Systematic search calculations using various 2D fingerprints to analyze search performance.

Main Results:

  • Most investigated 2D fingerprints successfully differentiated peptide-like molecules based on activity.
  • Two distinct 2D fingerprints demonstrated a strong capability to identify molecules with decreasing peptide character.
  • A property descriptor-based fingerprint showed adaptability in recovering molecules with low peptide-likeness, irrespective of molecular size.

Conclusions:

  • 2D fingerprints are effective tools for similarity searching of peptide-like molecules, aiding in activity differentiation.
  • Specific fingerprints, particularly property descriptor-based ones, are promising for guiding peptidomimetic drug design.
  • The "peptide flavor" index provides a valuable metric for characterizing peptide-like compounds in drug discovery.