Identification of ligand features essential for HDACs inhibitors by pharmacophore modeling

Histone deacetylases (HDACs) enzyme plays a significant role in transcriptional regulation by modifying the core histones of the nucleosome. It has emerged as an important therapeutic target for the treatment of cancer and other diseases. Inhibitors of HDACs become a new class of anticancer agents and have provoked much interest amongst pharmacologists and cancer researchers. To facilitate the discovery of specific HDACs inhibitors, a 3D chemical-feature-based QSAR pharmacophore model was developed and was well consistent with the structure-functional requirements for the binding of the HDAC inhibitors. Using this model, the interactions between the benzamide MS-275 and HDAC were explored. The result showed that the type and spatial location of chemical features encoded in the pharmacophore are in full agreement with the enzyme-inhibitor interaction pattern identified from molecular docking.