2.3. Docking studies

Molecular docking was performed using Biovia’s Discovery studio 4.0 software using the Dock ligands (CDOCKER) protocol which is an implementation of the CDOCKER algorithm. The X-ray crystal structure of the kinase domain of HDAC6 in complex with its propionic acid derivative inhibitor (PDB entry 5G0H) was recovered from RSCB protein data bank. The protein structure was prepared using protein preparation protocol of Biovia’s discovery studio 4.0. The amino acid residues were ionised using role-based technique and the missing residues and hydrogen atoms were added and minimised. The protein structure was typed by CHARMM. Synthesised compounds were prepared from ligands prepare tool which fix bad valences, adds hydrogen, and generates a 3 D coordinates using catalyst. Docking was performed using (CDOCKER) protocol. Top hits were set to 10 and pose cluster radius was set to 0.5 Å, while other docking parameters were kept as default. The best docking poses are analyzed according to docking score and interactions with key amino acids of the receptor using CDOCKER_ENERGY scoring function.