Structure similarity based screening coupled to integrated structural biochemistry approach for exploring the high affinity inhibitors against histone deacetylase (HDAC)-6.

Histone deacetylase (HDAC)-6 has overwhelming implications in multiple cancers and neurodegenerative disorders. Unusual HDAC6 expression modulates various signalling mechanisms which in turn forms the aetiology of the above-mentioned disorders. Thus, restoring the typical activity of HDAC6 through small molecules may prove as a promising approach to beat these disorders. Herein, we employed an integrated approach for exploring the high binding affinity manifesting molecules against HDAC6. We screened the entire PubChem database using Tubastatin A as the reference (query) molecule following which we carried out 110 molecular docking (XP-mode) and 110 MM-GBSA experiments. Thirty-three molecules demonstrated raised binding affinity than query in the HDAC6 active site. Further, the top 3 binders selected on logical grounds were subjected to interaction study, two hit molecules and tubastatin-A were subjected to convoluted molecular dynamics and three-dimensional e-Pharmacophores mapping was done to delineate the rationale behind the high binding tendency of hit molecules over control molecule. This work provides a solid foundation for additional research towards the development of lead molecules from the said hits for therapeutic intervention against HDAC6 overexpression-driven disorders.