ArticleInternational journal of molecular sciences2024
Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.
Article in International journal of molecular sciences, 2024. 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, 20 citations in OpenAlex.
- Inhibiting NHEJ: In-Silico Approach to Stratifying DNA-PK Inhibitors, Predicting Radio-Halogenation Potential of DNA-PK Inhibitors, and Assessing AlphaFold2 Prediction Accuracy.Bioengineering (Basel, Switzerland) · 2026Article
- Discovery of Novel Chemotype LRRK2 Inhibitors Through AlphaFold2-Generated Structure-Based Docking Screen.International journal of molecular sciences · 2026Article
- Cellular Target Engagement and Dissociation Kinetics of Class I-Selective Histone Deacetylase (HDAC) Inhibitors.International journal of molecular sciences · 2026Article
- AlphaFold for Docking Screens.Methods in molecular biology (Clifton, N.J.) · 2026Article
- An integrative omics-guided druggability analysis of VCX2 in hepatocellular carcinoma using Peruvian natural products.Frontiers in bioinformatics · 2026Article
- AI-identified CD133-targeting natural compounds demonstrate differential anti-tumor effects and mechanisms in pan-cancer models.EMBO molecular medicine · 2025Article
- Substrate-Guided Development of HDAC11-Selective Inhibitors Featuring α‑Amino Amide Zinc-Binding Groups.ACS omega · 2025Article
- Leveraging AlphaFold2 structural space exploration for generating drug target structures in structure-based virtual screening.Biochemistry and biophysics reports · 2025Article
- Heteroaryl-Capped Hydroxamic Acid Derivatives with Varied Linkers: Synthesis and Anticancer Evaluation with Various Apoptosis Analyses in Breast Cancer Cells, Including Docking, Simulation, DFT, and ADMET Studies.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Discovery and Characterization of Novel Non-Hydroxamate HDAC11 Inhibitors.International journal of molecular sciences · 2025Article
- Molecular Docking, Molecular Dynamics Simulation, and Pharmacophore-Based Virtual Screening Unveil Natural Compounds with TIM-3 Inhibitory Activity.Journal of pharmacy & bioallied sciences · 2025Article
- Computational insights into the targeted inhibition of lipoxygenase in Pseudomonas aeruginosa: hints for drug design.Archives of microbiology · 2025Article
- Enhancing HDAC Inhibitor Screening: Addressing Zinc Parameterization and Ligand Protonation in Docking Studies.International journal of molecular sciences · 2025Article
- Reliability of AlphaFold2 Models in Virtual Drug Screening: A Focus on Selected Class A GPCRs.International journal of molecular sciences · 2024Article
- The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods.Pharmaceuticals (Basel, Switzerland) · 2024Review
- Discovery of a Novel Chemo-Type for TAAR1 Agonism via Molecular Modeling.Molecules (Basel, Switzerland) · 2024Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
HDAC11 is a class IV histone deacylase with no crystal structure reported so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms, which makes conventional homology modeling less reliable. AlphaFold is a machine learning approach that can predict the 3D structure of proteins with high accuracy even in absence of similar structures. However, the fact that AlphaFold models are predicted in the absence of small molecules and ions/cofactors complicates their utilization for drug design. Previously, we optimized an HDAC11 AlphaFold model by adding the catalytic zinc ion and minimization in the presence of reported HDAC11 inhibitors. In the current study, we implement a comparative structure-based virtual screening approach utilizing the previously optimized HDAC11 AlphaFold model to identify novel and selective HDAC11 inhibitors. The stepwise virtual screening approach was successful in identifying a hit that was subsequently tested using an in vitro enzymatic assay. The hit compound showed an IC
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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.