Inhibition and mechanism of HDAC8 revisited

Abstract

Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure-activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.

Figure 1

HDAC8-substrate complex crystal structure 2V5W (Y306F mutation is manually removed). The oxygen atom of water is shown as red sphere, Zn²⁺ and K⁺ are represented by gray and purple spheres, respectively. Substrate and residues considered in the QM/MM active sites are shown as sticks, other residues are shown in green cartoon.

Scheme 1. HDAC Deacetylation Reaction Mechanism Proposed by Finnin et al. (Mechanism 1) and Zhang et al. (Mechanism 2)^,

Figure 2

(A) crystal structure of HDAC8 (pdb code: 2V5W) with active-site Zn²⁺ and two K⁺ ions and K⁺ binding (B) site 1 and (C) site 2. Zn²⁺ and K⁺ are shown as gray and purple spheres, respectively.

Figure 3

QM regions of models 1 (left) and 2 (right) shown for the optimized structures of SAHA-HDAC8 complex. Blue lines indicate the QM/MM boundary region.

Figure 4

Energy change during O–H distance scan for two active site models.

Figure 5

QM/MM deacetylation mechanism of HDAC. Energies (ONIOM(M052X/(6-31G*, SDD):AMBER), in kcal/mol) of optimized structures without or with (in parentheses) the presence of potassium at site 1 using the initial conformations from minimized structures of crystal structure without or with potassium at site 1.

Figure 6

Optimized structures of selected stationary points without the presence of potassium at site 1.

Figure 7

Optimized structures of selected stationary points with the presence of potassium at site 1; apostrophe symbol indicates the presence of potassium at site 1.