Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study

Abstract

Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding toward class IIa HDACs.

Keywords: HDAC; QM/MM; Zinc enzyme; inhibitor; molecular dynamics.

Figure 1

(a) Complete free energy profile for the deprotonation of SAHA determined by ab initio QM/MM MD simulation and umbrella sampling for small standard QM system (b) Complete free energy profile for the deprotonation of SAHA for enlarged system which include D176 and D183. (d2–d1) was chosen as reaction coordinate. d1 is the distance between SAHA: H (on O1) and H142: N^ε. d2 is the distance between SAHA: O1 and SAHA: H (on O1). The statistical error is estimated by averaging the free energy difference between 5–15ps and 15–25ps.

Figure 2

Complete free energy profile for the transition between HIP143 and HIP142 state in HDAC8 system determined by ab initio QM/MM MD simulation and umbrella sampling. The reaction coordinate is chosen as (d4–d3). d4 is the distance between H143: N^ε and H143: H (on N^ε), d3 is the distance between H143: H (on N^ε) and oxygen of the water molecule between H142 and S_SAHA. The statistical error is estimated by averaging the free energy difference between 5–15ps and 15–25ps. The detailed structural characterization is shown in Figure S4 of Supporting Information.

Figure 3

Complete free energy profile for the transition between negative S_SAHA and neutral S_SAHA state in HDAC8 system determined by ab initio QM/MM MD simulation and umbrella sampling. The reaction coordinate is chosen as −d2. d2 is distance between H143: H (on N^ε) and S_SAHA: S1. The statistical error is estimated by averaging the free energy difference between 5–15ps and 15–25ps.

Figure 4

(a) Binding site of HDAC8-SAHA complex. (b) Binding site of HDC8-S_SAHA complex. All the distance is from 55ps unrestrained QM/MM MD simulation. The Zinc is shown in the light yellow sphere and sulfur is shown in the dark yellow sphere. All hydrogen bonds are shown in magenta dashed line.

Figure 5

(a) Binding site of HDAC8-S_SAHA complex. (b) Binding site of HDAC4-S_SAHA complex. All the distance is from 55ps unrestrained QM/MM MD simulation. The Zinc is shown in the purple sphere and sulfur is shown in the dark yellow sphere. All hydrogen bonds are shown in magenta dashed line.

Figure 6

(a) Pocket view of HDAC8-S_SAHA complex. (b) Pocket view of HDAC4-S_SAHA complex. Zinc is shown in gray sphere.

Figure 7

Integrated water number around sulfur atoms of S_SAHA. The x-axis is the distance between the oxygen of water molecule and sulfur atom of S_SAHA.