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. 2025 Dec;40(1):2468355.
doi: 10.1080/14756366.2025.2468355. Epub 2025 Feb 27.

Design and synthesis of novel HDAC6 inhibitor dimer as HDAC6 degrader for cancer treatment by palladium catalysed dimerisation

Ching Lin  1 , Jui-Ling Hsu  1   2   3 , Yu-Tung Hsu  1 , Kuo-Chen Fan  1 , Sian-Siou Wu  1 , Miao-Hsia Lin  4 , Jih-Hwa Guh  1 , Chao-Wu Yu  1
Affiliations

Design and synthesis of novel HDAC6 inhibitor dimer as HDAC6 degrader for cancer treatment by palladium catalysed dimerisation

Ching Lin et al. J Enzyme Inhib Med Chem. 2025 Dec.

Abstract

The enigmatic histone deacetylase 6 (HDAC6) is one of a kind among its family. Recent reports revealed that HDAC6 CD1 exhibits E3 ligase activity. Inspired by these researches, we attempted to develop drugs targeting HDAC6 via novel mechanism. Herein, we report a palladium catalysed transformation and purification method for hydroxamic acid dimers, and series of HDAC6 inhibitor-based dimer showing outstanding biological activities and capability of inducing auto-degradation. Our proof-of-concept was highlighted with 2-amino benzamide-based HDAC6 inhibitor dimers that exhibit great HDAC6 inhibition activity (3.9-15.4 nM), good HDAC1/6 selectivity (95-577), and excellent cytotoxicity against human hormone-resistant prostate cancer (HRPC) PC-3 and non-small cell lung cancer (NSCLC) A549 cell lines (5.9-11.3 and 6.6-17.9 μM, respectively) while simultaneously inducing HDAC6 degradation. These dimers not only induce apoptosis and autophagy but also interfere with kinetochore attachment by the detection of BUBR1 phosphorylation at S670.

Keywords: HDAC6; anticancer; coupling; palladium; protein degrader.

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Conflict of interest statement

No potential conflict of interest was reported by the authors.

Figures

None
Graphical abstract
Figure 1.
Figure 1.
Working hypothesis of HDAC6 degrading dimers.
Scheme 1.
Scheme 1.
Synthesis of compounds 2a and 2b. Reagents and conditions: (a) Phenethylamine, EtOAc, rt, 1 h; (b) CDI, EtOAc, rt, 19 h; (c) K2CO3, methyl 4-(bromomethyl)benzoate, acetone, 60 °C, 3 h.
Scheme 2.
Scheme 2.
Synthesis of compounds 4a–c. Reagents and conditions: (a) Diamine, Cs2CO3, μ-OMs dimer, BrettPhos, dioxane, reflux, 24 h; (b) NH2OH in THF/CH2Cl2/MeOH (2 M), rt, 2 h.
Scheme 3.
Scheme 3.
Synthesis of compounds 6a–c. Reagents and conditions: (a) Diamine, Cs2CO3, μ-OMs dimer, BrettPhos, dioxane, reflux, 24 h; (b) NH2OH in THF/CH2Cl2/MeOH (2 M), rt, 2 h.
Scheme 4.
Scheme 4.
Synthesis of compounds 8a–c. Reagents and conditions: (a) Diamine, EtOAc, rt, 1 h; (b) CDI, EtOAc, rt, 19 h; (c) K2CO3, methyl 4-(bromomethyl)benzoate, DMF, rt, 2 h; (d) NH2OH in THF/CH2Cl2/MeOH (2 M), rt, 2 h.
Scheme 5.
Scheme 5.
Synthesis of Compounds 11a–c. Reagents and conditions: (a) K2CO3, methyl 4-(bromomethyl)benzoate, DMF, rt, 2 h; (b) Diamine, EtOAc, rt, 1 h; (c) Diamine, DMAC, MW 250 W, reflux, 12 min; (d) NH2OH in THF/CH2Cl2/MeOH (2 M), rt, 2 h
Figure 2.
Figure 2.
Molecular docking analysis of 1 to hHDAC6 CD2 via MOE. (Left) Interaction diagram of 1 with the binding pocket. (Right) Top-down view of 1 docking to hHDAC6 CD2 with the receptor coloured in pink. (PDB ID: 5EDU).
Figure 3.
Figure 3.
Western blotting analysis of (a) HDAC6 protein in PC-3 cells treated with various dimer compounds at 30 μM for 24 h, (b) Ac-α-tubulin protein in PC-3 cells treated with various dimer compounds at 30 μM for 24 h, (c) LC-3 I, LC-3 II, and p62 proteins in PC-3 cells treated with various dimer compounds at 30 μM for 24 h, (d) PARP-1 and Caspase-3 proteins in PC-3 cells treated with various dimer compounds at 30 μM for 24 h, (e) p-BUBR1S670 and p-BUBR1T680 proteins in PC-3 cells treated with various dimer compounds at 30 μM for 24 h. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was used as the loading control.
Figure 4.
Figure 4.
Molecular docking studies of 1 (coloured in pink) and 11a (coloured in cyan) to hHDAC6 CD2 under rigid receptor refinement via MOE. (PDB 5EDU).
Figure 5.
Figure 5.
Flow cytometric cell cycle analysis of PC-3 cells treated with various dimer compounds at 30 μM for 24 h.
Figure 6.
Figure 6.
Graphical conclusion of quinazolin-2,4-dione-based HDAC6 inhibitor dimers.
See this image and copyright information in PMC

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