Variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to HDAC8

Area of Science:

• Biochemistry
• Structural Biology
• Medicinal Chemistry

Background:

• Largazole is a macrocyclic depsipeptide and a potent inhibitor of metal-dependent histone deacetylases (HDACs).
• HDACs are drug targets for cancer chemotherapy, with Romidepsin (FK228) being a clinically approved example.
• The thiol group in Largazole coordinates to the active site Zn(2+) ion in HDAC8, a key feature for inhibition.

Purpose of the Study:

• To investigate the structural and binding characteristics of synthetic Largazole analogues with modified macrocycle skeletons.
• To explore how replacing the depsipeptide ester with an amide linkage and altering the thiazole ring affects HDAC8 inhibition.
• To elucidate new structure-affinity relationships for macrocyclic HDAC inhibitors.

Main Methods:

• X-ray crystallography was used to determine the structures of HDAC8 complexed with three synthetic Largazole analogues.
• Synthesis of Largazole analogues involved replacing the ester with an amide linkage and modifying the thiazole ring with a pyridine ring.
• Inhibitory potency of the analogues was compared to Largazole.

Main Results:

• X-ray crystal structures revealed that the thiol group of each analogue coordinates to the active site Zn(2+) ion in HDAC8 with excellent geometry.
• Analogues with amide linkages and pyridine ring substitutions preserved the key zinc-binding feature of Largazole.
• Despite structural modifications, the analogues exhibited inhibitory potency comparable to or moderately less than Largazole.
• The analogues induced alternative conformational changes in active site loops L1 and L2 compared to Largazole.

Conclusions:

• Synthetic Largazole analogues with amide linkages and modified macrocyclic rings retain significant HDAC8 inhibitory activity.
• The study reveals crucial structure-affinity relationships, demonstrating that modifications can alter binding conformations without drastically reducing potency.
• These findings provide valuable insights for the design of novel macrocyclic HDAC inhibitors for cancer therapy.