ArticleJournal of chemical information and modeling2023
Expanding Bioactive Fragment Space with the Generated Database GDB-13s.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Complete Computational Exploration of Eight-Carbon Hydrocarbon Chemical Space.The Journal of organic chemistry · 2026Article
- A View on Molecular Complexity from the GDB Chemical Space.Journal of chemical information and modeling · 2025Review
- Exploring Simple Drug Scaffolds from the Generated Database Chemical Space Reveals a Chiral Bicyclic Azepane with Potent Neuropharmacology.Journal of medicinal chemistry · 2025Article
- Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers.Molecular informatics · 2025Article
- One chiral fingerprint to find them all.Journal of cheminformatics · 2024Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying innovative fragments for drug design can help medicinal chemistry address new targets and overcome the limitations of the classical molecular series. By deconstructing molecules into ring fragments (RFs, consisting of ring atoms plus ring-adjacent atoms) and acyclic fragments (AFs, consisting of only acyclic atoms), we find that public databases of molecules (i.e., ZINC and PubChem) and natural products (i.e., COCONUT) contain mostly RFs and AFs of up to 13 atoms. We also find that many RFs and AFs are enriched in bioactive vs inactive compounds from ChEMBL. We then analyze the generated database GDB-13s, which enumerates 99 million possible molecules of up to 13 atoms, for RFs and AFs resembling ChEMBL bioactive RFs and AFs. This analysis reveals a large number of novel RFs and AFs that are structurally simple, have favorable synthetic accessibility scores, and represent opportunities for synthetic chemistry to contribute to drug innovation in the context of fragment-based drug discovery.
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Registered trials
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