Background: The epigenetic regulation of genes in cancer could be targeted by inhibiting Histone
deacetylase 6 (HDAC6), an enzyme involved in several types of cancer such as lymphoma, leukemia, ovarian
Objective: Through in silico methods, a set of Phenyl butyric acid derivatives with possible HDAC6 inhibitory
activity were designed, rendering monophenylamides and biphenylamides using tubacin (HDAC6 selective
inhibitor) as reference.
Method: The target compounds were submitted to theoretical ADMET analyses and their binding properties on
different HDAC6 conformers were evaluated through docking calculations.
Results: These in silico studies allowed us to identify a compound named B-R2B. In order to have more
information about the B-R2B binding recognition properties on HDAC6, the B-R2B-HDAC6 complex was
submitted through 100 ns-long Molecular Dynamics (MD) simulation coupled to MMGBSA approach, revealing
that B-R2B is located at the entrance of HDAC6 active pocket, blocking the passage of the substrate without
reaching the HDAC6 binding site. Based on these results, B-R2B was synthesized, characterized and biologically
tested. The HDAC6 fluorometric drug discovery kit Fluor-de-Lys (ENZO Life Sciences Inc.) was used to
determine the HDAC6 human inhibitory activity (IC50 value) of B-R2B compound. In addition, B-R2B show IC50
values on cancer cell lines (HeLa; IC50 = 72.6 µM), acute myeloid leukemia (THP-1; IC50 = 16.5 µM), human
mast leukemia (HMC; IC50 = 79.29 µM) and chronic myelogenous leukemia (Kasumi; IC50 = 101 µM).
Conclusion: These results show that B-R2B is a HDAC6 inhibitor, specifically a non-competitive type in a
similar way that tubacin does, according to MD simulations.