Background: A 3D-QSAR study of histone deacetylase 6 (HDAC6) inhibitors including
comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis
(CoMSIA) was carried out.
Method: Sixty-six compounds with their in vitro inhibitory activities (IC50 values) were first docked
into a homology model of HDAC6 using the LibDock program and then used to generate the training
and testing sets of compounds for both the CoMFA and CoMSIA studies.
Results and Conclusion: The best CoMFA model produced a q2 of 0.637 and an r2 of 0.987, and the
best CoMSIA model produced a q2 of 0.767 and an r2 of 0.987, indicating a high statistical
significance as a predictive model. The models and related information may provide important
insight into inhibitor–HDAC6 interactions and help in the design of novel potent HDAC inhibitors.
Keywords: HDAC6 inhibitors, 3D-QSAR, docking-based alignment, CoMFA, CoMSIA, compounds.
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