Structural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases

Abstract

Largazole is a macrocyclic depsipeptide originally isolated from the marine cyanobacterium Symploca sp., which is indigenous to the warm, blue-green waters of Key Largo, Florida (whence largazole derives its name). Largazole contains an unusual thiazoline-thiazole ring system that rigidifies its macrocyclic skeleton, and it also contains a lipophilic thioester side chain. Hydrolysis of the thioester in vivo yields largazole thiol, which exhibits remarkable antiproliferative effects and is believed to be the most potent inhibitor of the metal-dependent histone deacetylases (HDACs). Here, the 2.14 Å-resolution crystal structure of the HDAC8-largazole thiol complex is the first of an HDAC complexed with a macrocyclic inhibitor and reveals that ideal thiolate-zinc coordination geometry is the key chemical feature responsible for its exceptional affinity and biological activity. Notably, the core structure of largazole is conserved in romidepsin, a depsipeptide natural product formulated as the drug Istodax recently approved for cancer chemotherapy. Accordingly, the structure of the HDAC8-largazole thiol complex is the first to illustrate the mode of action of a new class of therapeutically important HDAC inhibitors.

Figure 1

The disulfide bond of romidepsin is reduced while the thioester linkage of largazole is hydrolyzed to form potent depsipeptide thiol inhibitors of HDACs. Structurally identical portions of each inhibitor are highlighted in red.

Figure 2

HDAC8-largazole thiol complex. The catalytic Zn²⁺ ion (red sphere) is coordinated by D178, H180, and D267 (blue sticks). Largazole thiol is shown as a stick figure (C = magenta, N = blue, O = red, and S = yellow). Structural K⁺ ions appear as green spheres.

Figure 3

(a) Simulated annealing omit map contoured at 3.0 σ (gray mesh) showing largazole thiol bound in the active site of monomer A; contours at 8.0 σ (blue mesh) confirm the positions of electron-rich sulfur atoms. Atoms are color-coded as in Fig. 2, and metal coordination interactions are indicated by black dotted lines. (b) Superposition of the HDAC8-largazole complex (blue; largazole is colored as in Fig. 2) and the HDAC8-substrate complex (cyan; PDB code 3EWF, less substrate atoms).

Figure 4

The experimentally determined structure of the HDAC8-largazole thiol complex (a) serves as a template for modeling the HDAC8-romidepsin thiol complex (b) simply by superimposing conserved depsipeptide features (i.e., the red portions of each inhibitor as illustrated in Fig. 1).