ArticleACS chemical biology2016
3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.
Article in ACS chemical biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 58 citations in OpenAlex.
- ComTarget: Small-Molecule Target Prediction with Combinatorial Modeling.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Discovery of Novel Chemotype LRRK2 Inhibitors Through AlphaFold2-Generated Structure-Based Docking Screen.International journal of molecular sciences · 2026Article
- Progress of AI-Driven Drug-Target Interaction Prediction and Lead Optimization.International journal of molecular sciences · 2025Review
- Next-Gen Therapeutics: Pioneering Drug Discovery with iPSCs, Genomics, AI, and Clinical Trials in a Dish.Annual review of pharmacology and toxicology · 2025Review
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
- The changing scenario of drug discovery using AI to deep learning: Recent advancement, success stories, collaborations, and challenges.Molecular therapy. Nucleic acids · 2024Review
- Computational Approaches to the Rational Design of Tubulin-Targeting Agents.Biomolecules · 2023Review
- Random-forest model for drug-target interaction prediction via Kullbeck-Leibler divergence.Journal of cheminformatics · 2022Article
- De Novo Prediction of Drug Targets and Candidates by Chemical Similarity-Guided Network-Based Inference.International journal of molecular sciences · 2022Article
- Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision.Journal of cheminformatics · 2021Article
- Comprehensive strategies of machine-learning-based quantitative structure-activity relationship models.iScience · 2021Review
- Recent Advances in In Silico Target Fishing.Molecules (Basel, Switzerland) · 2021Review
- Comparing a Query Compound with Drug Target Classes Using 3D-Chemical Similarity.International journal of molecular sciences · 2020Article
- Similarity-Based Methods and Machine Learning Approaches for Target Prediction in Early Drug Discovery: Performance and Scope.International journal of molecular sciences · 2020Article
- Dissecting the mechanisms of cell division.The Journal of biological chemistry · 2019Review
- Leukemia Cell Cycle Chemical Profiling Identifies the G2-Phase Leukemia Specific Inhibitor Leusin-1.ACS chemical biology · 2019Article
- Pocket similarity identifies selective estrogen receptor modulators as microtubule modulators at the taxane site.Nature communications · 2019Article
- Computational analysis of kinase inhibitor selectivity using structural knowledge.Bioinformatics (Oxford, England) · 2019Article
- Machine learning in chemoinformatics and drug discovery.Drug discovery today · 2018Review
- Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds.Frontiers in chemistry · 2018Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.