Cited by 806Computational Drug Discovery MethodsChemical Synthesis and AnalysisSynthesis and Characterization of Heterocyclic Compounds

Do Structurally Similar Molecules Have Similar Biological Activity?

Martin, Yvonne C., Kofron, James L., Traphagen, Linda M.·2002·Journal of Medicinal Chemistry

Abstract

To design diverse combinatorial libraries or to select diverse compounds to augment a screening collection, computational chemists frequently reject compounds that are > or =0.85 similar to one already chosen for the combinatorial library or in the screening set. Using Daylight fingerprints, this report shows that for IC(50) values determined as a follow-up to 115 high-throughput screening assays, there is only a 30% chance that a compound that is > or = 0.85 (Tanimoto) similar to an active is itself active. Although this enrichment is greater than that found with random screening and docking to three-dimensional structures, this low fraction of actives within similar compounds occurs not only because of deficiencies in the Daylight fingerprints and Tanimoto similarity calculations but also because similar compounds do not necessarily interact with the target macromolecule in similar ways. The current study emphasizes the statistical or probabilistic nature of library design and that perfect results cannot be expected.

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Crossref · 10.1021/jm020155c

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Authors
Martin, Y. C., Kofron, J. L., & Traphagen, L. M.
Affiliations
Abbott (United States) (US)
Corresponding author
Martin, Yvonne C.
Venue
Journal of Medicinal Chemistry
Published
2002-08-13
Volume
45
Issue
19
Pages
4350-4358
ISSN
  • 0022-2623 (ISSN-L)
  • 1520-4804
OpenAlex
W2156077095
Cited by
806
References
45
Citations by year
2026: 18 · 2025: 41 · 2024: 46 · 2023: 29 · 2022: 35 · 2021: 51 · 2020: 36 · 2019: 31 · 2018: 36 · 2017: 40 · 2016: 37 · 2015: 31 · 2014: 30 · 2013: 47 · 2012: 41
FWCI
16.10
Type
journal article
Language
en
Open access
closed
Locations
  • Journal of Medicinal Chemistry (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
  • Physical Sciences › Chemistry › Organic Chemistry › Synthesis and Characterization of Heterocyclic Compounds
Keywords
structural similarity, biological activity, combinatorial library design, Tanimoto similarity, high-throughput screening, IC50
MeSH terms
Data Interpretation, Statistical, Enzyme Inhibitors, Monoamine Oxidase Inhibitors, Molecular Structure, Databases, Factual, Combinatorial Chemistry Techniques, Quantitative Structure-Activity Relationship

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