Theoretical study of the catalytic mechanism and inhibition of histone deacetylase

Molecules that interfere with the activity of the enzyme HDAC (Histone Deacetylase), or HDAC Inhibitors, are part of a new generation of so-called mechanism-based anti-cancer drugs, that may combine clinical efficacy with relatively mild toxicological side-effects.[1,2] Medicinal applications of HDAC inhibitors are however not limited to the treatment of cancer, but may vary from fibrotic diseases,[3] including liver fibrosis,[4,5] an important cause of death in Western society, over autoimmune[6] and inflammatory[7] diseases, to polyglutamin disease.[8,9] Also, they have been shown to improve the preservation of cell cultures.[5] The present project aims to provide theoretical support for the development of new HDAC inhibitors. The structure of HDLP (Histone Deacetylase Like Protein, a bacterial HDAC analogue) in complex with TSA (Trichostatin A, the first potent HDAC inhibitor identified), was used as a starting point. This structure, elucidated by M. S. Finnin et al. using X-ray crystallography, provided the only available information about HDAC’s geometry at the start of this project.[10]In a first stage, the binding mode of different inhibitors in the active site of HDLP was investigated using molecular mechanics systematic conformational searches. Although the results of this work allowed us to rationalise the differences in potency between some inhibitors,[11] the method used is not adequate to describe the interactions between the inhibitor molecule and the zinc ion in the active site of the enzyme. Therefore, more refined techniques based on quantum mechanics had to be applied on at least part of the enzyme-inhibitor complex. For practical reasons, a method was chosen in which a relevant model of this complex is completely described at the Hartree-Fock quantum chemical level. To evaluate this approach, a geometry optimisation was performed on the HDLP-TSA complex. This calculation took a long time, but yielded a realistic binding geometry and energy.[12] It also provided insights into the protonation state of the zinc-binding part of inhibitor molecules, and indications were found that the enzyme’s mechanism of catalysis might differ slightly from the one proposed by M. S. Finnin et al. In order to gain more information about this catalytic mechanism, the catalytic core of the enzyme was investigated using Density Functional Theory, a level of calculation that is known to provide more accurate results than Hartree-Fock, especially when applied on metal complexes. The results of this study led to the proposal of an alternative catalytic mechanism.[13] In a final stage, the same catalytic core model and level of calculation were used to investigate the HDAC inhibitory potency of different zinc-binding groups that can be built into HDAC inhibitors.[14] The results of this study correlated reasonably with experimental data, indicating that the method is meaningful for the purpose of ranking. Sulfur-containing groups were shown to be viable alternatives for the commonly used hydroxamate groups. Also, a number of chemical properties was shown to have an important influence on the inhibitory potency, and consequently may be useful in the construction of QSAR models, which try to predict the medicinal potential of drug candidates based on molecular properties or descriptors. Finally, the catalytic core from the present study may be used in the future as part of a larger model encompassing the complete active site.[1] F. McLaughlin, P. Finn and N. B. La Thangue, Drug Discov. Today, 2003, 8, 793–802.[2] R. Warrener, H. Beamish, A. Burgess, N. J. Waterhouse, N. Giles, D. Fairlie and B. Gabrielli, FASEB J., 2003, 17, 1550–1552.[3] K. R