Do Structurally Similar Molecules Have Similar Biological Activity?
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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- Authors
- Martin, Y. C., Kofron, J. L., & Traphagen, L. M.
- Affiliations
- Abbott (United States) (US)
- Corresponding author
- Martin, Yvonne C.
- ORCID
- Martin, Yvonne C.
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- 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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