Difluoromethyl-1,3,4-oxadiazoles are selective, mechanism-based, and essentially irreversible inhibitors of histone deacetylase 6

04 September 2023, Version 4
This content is a preprint and has not undergone peer review at the time of posting.


Histone deacetylase 6 (HDAC6) is an important drug target in oncology and non-oncological diseases. Most available HDAC6 inhibitors (HDAC6i) utilize a hydroxamic acid as zinc-binding group which limits the therapeutic opportunities due 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 6 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 6 by the zinc-bound water at the sp2 carbon closest to the difluoromethyl moiety followed by a subsequent ring opening of the oxadiazole yields the deprotonated difluoroacetylhydrazide 13 as active species. The strong anionic zinc coordination of 13 and the binding of the difluoromethyl moiety in the P571 pocket finally results in an essentially irreversible inhibition of HDAC6.


histone deacetylase
enzyme kinetics

Supplementary materials

Electronic Supplementary Information
Supplementary Figures, Schemes, Equations and Tables, experimental procedures, 1H NMR, 13C NMR and MS data.


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.