Docking of hydroxamic acids into HDAC1 and HDAC8: a rationalization of activity trends and selectivities.
A docking protocol using Gold software was developed to predict the binding disposition of histone deacetylase (HDAC) inhibitors, starting from the X-ray structures of HDAC8. The optimized procedure was subsequently utilized to dock into HDAC8 and into a homology model of HDAC1 nearly 40 compounds that had been tested for their inhibitory activity against the two HDAC isozymes. Evaluation of the best binding poses allowed us to identify the ligand properties and the protein residues important for activity and selectivity. HDACs are important anticancer drug targets, and their study is currently being actively pursued. As such, our results could help design new isozyme-selective HDAC inhibitors. Furthermore, this strategy may also be used for the investigation of other HDACs.
Ortore
Gabriella
G
Dipartimento di Scienze Farmaceutiche, Universita di Pisa, via Bonanno 6, 56126 Pisa, Italy.
Di Colo
Francesco
F
Martinelli
Adriano
A
D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D056284:Histone Deacetylase 1 / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D056572:Histone Deacetylase Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D006655:Histone Deacetylases / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D006877:Hydroxamic Acids / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D021281:Quantitative Structure-Activity Relationship; D012097:Repressor Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D056572:Histone Deacetylase Inhibitors; D006877:Hydroxamic Acids; D008024:Ligands; D012097:Repressor Proteins; C409470:HDAC8 protein, human; D056284:Histone Deacetylase 1; D006655:Histone Deacetylases