Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States.
J Med Chem. 2023 Oct 12;66(19):13821-13837. doi: 10.1021/acs.jmedchem.3c01345. Epub 2023 Oct 2.
Histone deacetylase (HDAC6) is an important drug target in oncological and non-oncological diseases. Most available HDAC6 inhibitors (HDAC6i) utilize hydroxamic acids as a zinc-binding group, which limits therapeutic opportunities due to its genotoxic potential. Recently, difluoromethyl-1,3,4-oxadiazoles (DFMOs) were reported as potent and selective HDAC6i but their mode of inhibition remained enigmatic. Herein, we report that DFMOs act as mechanism-based and essentially irreversible HDAC6i. Biochemical data confirm that DFMO is a tight-binding HDAC6i capable of inhibiting HDAC6 via a two-step slow-binding mechanism. Crystallographic and mechanistic experiments suggest that the attack of by the zinc-bound water at the sp carbon closest to the difluoromethyl moiety followed by a subsequent ring opening of the oxadiazole yields deprotonated difluoroacetylhydrazide as active species. The strong anionic zinc coordination of and the binding of the difluoromethyl moiety in the P571 pocket finally result in an essentially irreversible inhibition of HDAC6.
组蛋白去乙酰化酶（HDAC6）是肿瘤和非肿瘤疾病中一个重要的药物靶点。大多数现有的 HDAC6 抑制剂（HDAC6i）都利用羟肟酸作为锌结合基团，但其遗传毒性潜力限制了其治疗机会。最近，二氟甲基-1,3,4-噁二唑（DFMOs）被报道为有效的、选择性的 HDAC6i，但它们的抑制机制仍然很神秘。在这里，我们报告说，DFMOs 是一种基于机制的、基本上不可逆的 HDAC6i。生化数据证实，DFMO 是一种紧密结合的 HDAC6i，能够通过两步慢结合机制抑制 HDAC6。晶体学和机制实验表明，锌结合水攻击离二氟甲基基团最近的 sp 碳原子，随后噁二唑环打开，生成带负电荷的二氟乙酰基酰肼 作为活性物质。DFMO 中强烈的阴离子锌配位和二氟甲基部分在 P571 口袋中的结合最终导致 HDAC6 的基本不可逆抑制。
