Examining the binding properties of some hydroxamic acid derivatives theoretically as a histone deacetylase (HDAC) inhibitor using the molecular docking method

In this study, the binding properties to enzyme active region of 59 hydoxamic acid derivetives of which inhibition activities were defined in literature before were investigated theoretically using Molecular Docking Method. Whole ligand molecules were optimized with DFT method in B3LYP/6-311G(d,p) level using G09 program. Quantum chemical parameters of optimized molecules were calculated such as total Energy, HOMO, LUMO, Egap, hardness (η), softness (S), Chemical Potential (μ), Electronegativity (χ), electrophilicity index (ω), İyonlaşma Potansiyeli (IP) and Elektron Afinitesi (EA). The relationship between calculated molecular descriptors and their inhibition activities were investigated. Docking poses and interactions of the ligand molecules at the enzyme active site were investigated using Molecular Docking Method. For this propose, various type of HDAC8 enzyme structure PDB ID: 1T64, 1T67, 1T69, 1W22, 4RN0 and 1WKG were downloaded from protein databank and molecular Docking studies were done using AutoDock Vina and Schrödinger Suite programs.