ArticleJournal of medicinal chemistry2022
Fragment Libraries Designed to Be Functionally Diverse Recover Protein Binding Information More Efficiently Than Standard Structurally Diverse Libraries.
Article in Journal of medicinal chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- FRAIL: fragment-based reinforcement learning for molecular design and benchmarking on fatty acid amide hydrolase 1 (FAAH-1).Molecular diversity · 2026Article
- Developments and challenges in hit progression within fragment-based drug discovery.Nature communications · 2026Review
- Article
- Medicinal Chemistry behind Capivasertib Discovery: Seventh Magic Bullet of the Fragment-based Drug Design Approved for Oncology.Current medicinal chemistry · 2025Review
- FGTN: Fragment-based graph transformer network for predicting reproductive toxicity.Archives of toxicology · 2024Article
- Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them.Acta crystallographica. Section D, Structural biology · 2024Article
- Building Block-Centric Approach to DNA-Encoded Library Design.Journal of chemical information and modeling · 2024Article
- DrugGym: A testbed for the economics of autonomous drug discovery.bioRxiv : the preprint server for biology · 2024Article
- Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.Science (New York, N.Y.) · 2023Article
- Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search.Journal of chemical information and modeling · 2023Article
- Ultrafast Fragment Screening Using Photo-Hyperpolarized (CIDNP) NMR.Journal of the American Chemical Society · 2023Article
- A Small Step Toward Generalizability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening.Journal of chemical information and modeling · 2023Article
- Mining the Protein Data Bank to inspire fragment library design.Frontiers in chemistry · 2023Article
- Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery.Pharmaceuticals (Basel, Switzerland) · 2022Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current fragment-based drug design relies on the efficient exploration of chemical space by using structurally diverse libraries of small fragments. However, structurally dissimilar compounds can exploit the same interactions and thus be functionally similar. Using three-dimensional structures of many fragments bound to multiple targets, we examined if a better strategy for selecting fragments for screening libraries exists. We show that structurally diverse fragments can be described as functionally redundant, often making the same interactions. Ranking fragments by the number of novel interactions they made, we show that functionally diverse selections of fragments substantially increase the amount of information recovered for unseen targets compared to the amounts recovered by other methods of selection. Using these results, we design small functionally efficient libraries that can give significantly more information about new protein targets than similarly sized structurally diverse libraries. By covering more functional space, we can generate more diverse sets of drug leads.
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