ArticleInternational journal of molecular sciences2011
Dynamic structure-based pharmacophore model development: a new and effective addition in the histone deacetylase 8 (HDAC8) inhibitor discovery.
Article in International journal of molecular sciences, 2011. 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, 47 citations in OpenAlex.
- Crucial Structural Understanding for Selective HDAC8 Inhibition: Common Pharmacophores, Molecular Docking, Molecular Dynamics, and Zinc Binder Analysis of Selective HDAC8 Inhibitors.Medicinal chemistry (Shariqah (United Arab Emirates)) · 2025Review
- Unveiling critical structural features for effective HDAC8 inhibition: a comprehensive study using quantitative read-across structure-activity relationship (q-RASAR) and pharmacophore modeling.Molecular diversity · 2024Article
- The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods.Pharmaceuticals (Basel, Switzerland) · 2024Review
- In the quest for histone deacetylase inhibitors: current trends in the application of multilayered computational methods.Amino acids · 2023Review
- γ-Secretase Inhibitors Selected by Molecular Docking, to Develop a New Drug Against Alzheimer's Disease.Reports of biochemistry & molecular biology · 2023Article
- Identification of Selective BRD9 Inhibitor via Integrated Computational Approach.International journal of molecular sciences · 2022Article
- Potential inhibitors interacting in Neuropilin-1 to develop an adjuvant drug against COVID-19, by molecular docking.Bioorganic & medicinal chemistry · 2021Article
- Identification of unique subtype-specific interaction features in Class II zinc-dependent HDAC subtype binding pockets: A computational study.Journal of biosciences · 2021Article
- Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles.Journal of computer-aided molecular design · 2020Article
- Potential inhibitors of the interaction between ACE2 and SARS-CoV-2 (RBD), to develop a drug.Life sciences · 2020Article
- Discovery of novel potential selective HDAC8 inhibitors by combine ligand-based, structure-based virtual screening and in-vitro biological evaluation.Scientific reports · 2019Article
- HDAC11 Inhibits Myoblast Differentiation through Repression of MyoD-Dependent Transcription.Molecules and cells · 2017Article
- Virtual screening and experimental validation of novel histone deacetylase inhibitors.BMC pharmacology & toxicology · 2016Article
- Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules.Journal of chemical information and modeling · 2015Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this enzyme has emerged as an efficient cancer therapeutic strategy. In an effort to facilitate the future discovery of HDAC8 inhibitors, we developed two pharmacophore models containing six and five pharmacophoric features, respectively, using the representative structures from two molecular dynamic (MD) simulations performed in Gromacs 4.0.5 package. Various analyses of trajectories obtained from MD simulations have displayed the changes upon inhibitor binding. Thus utilization of the dynamically-responded protein structures in pharmacophore development has the added advantage of considering the conformational flexibility of protein. The MD trajectories were clustered based on single-linkage method and representative structures were taken to be used in the pharmacophore model development. Active site complimenting structure-based pharmacophore models were developed using Discovery Studio 2.5 program and validated using a dataset of known HDAC8 inhibitors. Virtual screening of chemical database coupled with drug-like filter has identified drug-like hit compounds that match the pharmacophore models. Molecular docking of these hits reduced the false positives and identified two potential compounds to be used in future HDAC8 inhibitor design.
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