ArticleScientific reports2018
Scaffold-Hopping from Synthetic Drugs by Holistic Molecular Representation.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 45 citations in OpenAlex.
- Advancing toxicity AI-based prediction with multilevel systems biology: a case study on genotoxicity.Briefings in bioinformatics · 2025Article
- Going beyond SMILES enumeration for data augmentation in generative drug discovery.Digital discovery · 2025Article
- Recent advances in molecular representation methods and their applications in scaffold hopping.npj drug discovery · 2025Review
- Prediction of Dielectric Constant in Series of Polymers by Quantitative Structure-Property Relationship (QSPR).Polymers · 2024Article
- Drug-Target Interactions Prediction at Scale: The Komet Algorithm with the LCIdb Dataset.Journal of chemical information and modeling · 2024Article
- Scaffold-Hopped Compound Identification by Ligand-Based Approaches with a Prospective Affinity Test.Journal of chemical information and modeling · 2024Article
- Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms.Journal of cheminformatics · 2024Article
- Exposing the Limitations of Molecular Machine Learning with Activity Cliffs.Journal of chemical information and modeling · 2022Article
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- De Novo Molecular Design with Chemical Language Models.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Deep scaffold hopping with multimodal transformer neural networks.Journal of cheminformatics · 2021Article
- Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease.Molecules (Basel, Switzerland) · 2021Article
- Molecular Scaffold Hopping via Holistic Molecular Representation.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Novel Small-Molecule Scaffolds as Candidates against the SARS Coronavirus 2 Main Protease: A Fragment-Guided in Silico Approach.Molecules (Basel, Switzerland) · 2020Article
- Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships.Journal of computer-aided molecular design · 2019Article
- From genetic causality to druggable targets: A multiomics framework identifies ZSCAN16 in gout pathogenesis.Science progressArticle
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The discovery of novel ligand chemotypes allows to explore uncharted regions in chemical space, thereby potentially improving synthetic accessibility, potency, and the drug-likeness of molecules. Here, we demonstrate the scaffold-hopping ability of the new Weighted Holistic Atom Localization and Entity Shape (WHALES) molecular descriptors compared to seven state-of-the-art molecular representations on 30,000 compounds and 182 biological targets. In a prospective application, we apply WHALES to the discovery of novel retinoid X receptor (RXR) modulators. WHALES descriptors identified four agonists with innovative molecular scaffolds, populating uncharted regions of the chemical space. One of the agonists, possessing a rare non-acidic chemotype, revealed high selectivity on 12 nuclear receptors and comparable efficacy as bexarotene on induction of ATP-binding cassette transporter A1, angiopoietin like protein 4 and apolipoprotein E. The outcome of this research supports WHALES as an innovative tool to explore novel regions of the chemical space and to detect novel bioactive chemotypes by straightforward similarity searching.
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