Bornes Kiara E, Moody Marcus A, Huckaba Thomas M, Benz Megan C, McConnell Emily C, Foroozesh Maryam, Barnes Van H, Collins-Burow Bridgette M, Burow Matthew E, Watt Terry J, Toro Tasha B
Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA.
Tulane University School of Medicine, New Orleans, LA, USA.
FEBS Open Bio. 2025 Jan;15(1):94-107. doi: 10.1002/2211-5463.13896. Epub 2024 Oct 31.
Lysine deacetylases (KDACs or HDACs) are metal-dependent enzymes that regulate lysine acetylation, a post-translational modification that is present on thousands of human proteins, essential for many cellular processes, and often misregulated in diseases. The selective inhibition of KDACs would allow for understanding of the biological roles of individual KDACs and therapeutic targeting of individual enzymes. Recent studies have suggested that purportedly specific KDAC inhibitors have significant off-target binding, but the biological consequences of off-target binding were not evaluated. We compared the effects of treatment with two of the reportedly most KDAC-selective inhibitors, Tubastatin A and PCI-34051, in HT1080 cells in which the endogenous KDAC6 or KDAC8 gene has been mutated to inactivate enzyme catalysis while retaining enzyme expression. Genetic inactivation results in much stronger deacetylation defects on known targets compared to inhibitor treatment. Gene expression analysis revealed that both inhibitors have extensive and extensively overlapping off-target effects in cells, even at low inhibitor doses. Furthermore, Tubastatin A treatment led to increased histone acetylation, while inactivation of KDAC6 or KDAC8 did not. Genetic inactivation of KDAC6, but not KDAC8, impaired tumor formation in a xenograft model system, in contrast to previous reports with KDAC inhibitors suggesting the reverse. We conclude that the majority of observed biological effects of treatment with KDAC inhibitors are due to off-target effects rather than the intended KDAC inhibition. Developing a truly specific KDAC6 inhibitor could be a promising therapeutic avenue, but it is imperative to develop new inhibitors that selectively mimic genetic inactivation of individual KDACs.
赖氨酸脱乙酰酶（KDACs或HDACs）是金属依赖性酶，可调节赖氨酸乙酰化，这是一种存在于数千种人类蛋白质上的翻译后修饰，对许多细胞过程至关重要，且在疾病中常出现调控异常。选择性抑制KDACs将有助于了解单个KDACs的生物学作用以及对单个酶进行治疗靶向。最近的研究表明，据称具有特异性的KDAC抑制剂存在显著的脱靶结合，但未评估脱靶结合的生物学后果。我们比较了两种据报道对KDAC选择性最高的抑制剂Tubastatin A和PCI-34051对HT1080细胞的处理效果，在这些细胞中，内源性KDAC6或KDAC8基因已发生突变，以在保留酶表达的同时使酶催化失活。与抑制剂处理相比，基因失活导致已知靶点上的去乙酰化缺陷更强。基因表达分析显示，即使在低抑制剂剂量下，两种抑制剂在细胞中都具有广泛且广泛重叠的脱靶效应。此外，Tubastatin A处理导致组蛋白乙酰化增加，而KDAC6或KDAC8失活则没有。与之前关于KDAC抑制剂的报道相反，KDAC6基因失活而非KDAC8基因失活在异种移植模型系统中损害了肿瘤形成。我们得出结论，KDAC抑制剂处理所观察到的大多数生物学效应是由于脱靶效应而非预期的KDAC抑制。开发一种真正特异性的KDAC6抑制剂可能是一条有前景的治疗途径，但开发能够选择性模拟单个KDACs基因失活的新抑制剂势在必行。
