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.

Histone deacetylases: structural determinants of inhibitor selectivity

“…Briefly, an ion bound to site 2 has been proposed to stabilize the active conformation of HDAC8 by acting as an allosteric effector, whereas an ion bound to site 1 has been suggested to reduce the catalytic activity by decreasing the pK a of His142 (corresponding to H669 in HDAC7, numbering based on HDAC8). A recent computational study also supported the finding that catalytic activity is inhibited by the presence of K + at site 1 [66]. The role of His142 in K + inhibition is further supported by the finding that the H142A mutant was not inhibited by K + [65].…”

“…However, upon coordination of the zinc ion, the pK a of hydroxamic acids would be reduced by approximately three units, the acidic proton being transferred to the adjacent conserved histidine (H669 in HDAC7) [80]. Interestingly, computational studies [41,66,[81][82][83] indicate that the anionic hydroxamate chelates the zinc ion in a bidentate fashion with geometries close to the experimental ones. However, whether the hydroxamic acids bind HDAC by adopting a neutral or anionic form is still matter of debate, and further investigations will be necessary to draw more definitive conclusions.…”

Inhibition mechanism of SAHA in HDAC: a revisit

“…Intriguingly, the second metal site in HDAC2 is distinct from HDAC8 and HDAC7 (Ca 2+ in HDAC2 but K + in HDAC8/7, see Figure 1), and this conserved metal binding site in HDAC is related to its catalytic activity experimentally. 18,[20][21][22] It should be clearly emphasized that the K + ion in the second metal site (~7Å from the catalytic center Zn 2+ , see Figure 1) is kept in our previous modelling as most experiments had proved it to be conserved, whereas it is absent in Wiest's model. In this sense, it is unwarranted to compare our previous simulations with Wiest's modelling on HDAC8, since the employed computational models are different not only in terms of their number of atoms in the QM region, but also their choice of theoretical method (QM/MM MD vs static ONIOM).…”

Histone Deacetylase 8: Characterization of Physiological Divalent Metal Catalysis

“…To additionally assess the role of the K + binding site as a whole, a significantly contracted active site was built; it contained the side chains of the residues H142, H143, D178, H180, D267, Y306, D176, and D183 (numbering as in the pdb structure 2V5W), resembling the previously published model by Chen et al 60 ( Figure 4, blue and green residues). In general, the rate-limiting transition state was stabilized by an additional 3−4 kcal/mol.…”

“…The contributions the catalytic dyad contacts lend toward HDAC8 catalysis have been a matter of discussion. 60 An even more contracted QM site was constructed to characterize the effect of the H142−D176 and H143−D267 dyad contacts. This site excluded the D176 and D267 dyad residues.…”