Computational and Pharmacological Characterization of HDAC6 Inhibition and Function

  • Aaron Maguire

Student thesis: Doctoral ThesisDoctor of Philosophy


HDAC6 is a unique histone deacetylase. It contains two catalytic domains, of which they act independently or in tandem. It belongs to the class IIb HDACs and is Zn2+ dependant. It has been seen to be involved in various diseases such as diabetic neuropathies and certain cancers including breast cancer and high grade serous ovarian cancer. There are numerous HDAC inhibitors that can inhibit HDAC6. These include Trichostatin A and Vorinostat. Recently there has been a drive towards HDAC6 specific inhibitors due to its presence in these diseases. These inhibitors include Nexturastat A and Ricolinostat (ACY-1215). Within this thesis these four inhibitors have been used extensively.

The recent publication of Danio rerio HDAC6 crystal structures by Miyake et al and Hai et al has allowed for molecular dynamics simulations to be conducted alongside in vitro laboratory experiments. The main focus, from an in silico perspective, of this thesis is to understand the molecular conformations of human HDAC6 catalytic domains as monomers and as a dimer obtained from atomistic explicit solvent simulations. The dynamics of five main active site loops involving L1, L2, L3, L4 and L5 have been explored. Protein correlation networks from computer trajectories are created to understand residue communication in both the monomer and dimer forms. Inhibitor – residue interactions are also monitored and important residues, in particular H139, H140, H610 and H611 for inhibitor binding are uncovered in both domains. In addition, π-π aromatic stacking interactions are also observed between W208 (CD1) or F680 (CD2) and the terminal CAP segment of the inhibitors. Potential binding cavities have been mapped that will, hopefully, allow for further inhibition of HDAC6 outside of the active sites in both catalytic domains. The interface between the domains has also been characterised and two residues identified as being potentially important for domain – domain communication (Q314 and D267).

In vitro mutations of F629 were conducted within this thesis to understand the importance of the stacking interactions with the inhibitor. Newly isolated cell lines, SMGs, were characterised to be high grade serous ovarian cancer and tested with common chemotherapies; paclitaxel and cisplatin both as monotherapies and in combination with ACY-1215. Here, it can be concluded that ACY-1215 has no effect on proliferation at its specific HDAC6 dose of 1 µM, however, it may cause a decrease in migration. It is also demonstrated that HDAC6 knockdown will affect both proliferation and migration of the SMG cell lines. Overall, it can be concluded that HDAC6 is a promising novel target for cancer therapy.
Date of AwardDec 2020
Original languageEnglish
Awarding Institution
  • Queen's University Belfast
SupervisorIrina Tikhonova (Supervisor) & Fiona Furlong (Supervisor)

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