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Title: Comprehensive mechanistic view of the hydrolysis of oxadiazole-based inhibitors by Histone Deacetylase 6 (HDAC6)
Author(s): Motlová, Lucia
Šnajdr, Ivan
Kutil, Zsófia
Andris, Erik
Ptáček, Jakub
Novotná, Adéla
Nováková, Zora
Havlínová, Barbora
Tueckmantel, Werner
Dráberová, Helena
Majerčiak, PavelLook up in the Integrated Authority File of the German National Library
Schutkowski, Mike
Kozikowski, Alan
Rulíšek, Lubomir
Bařinka, Cyril
Issue Date: 2023
Type: Article
Language: English
Abstract: Histone deacetylase (HDAC) inhibitors used in the clinic typically contain a hydroxamate zinc-binding group (ZBG). However, more recent work has shown that the use of alternative ZBGs, and, in particular, the heterocyclic oxadiazoles, can confer higher isoenzyme selectivity and more favorable ADMET profiles. Herein, we report on the synthesis and biochemical, crystallographic, and computational characterization of a series of oxadiazole-based inhibitors selectively targeting the HDAC6 isoform. Surprisingly, but in line with a very recent finding reported in the literature, a crystal structure of the HDAC6/inhibitor complex revealed that hydrolysis of the oxadiazole ring transforms the parent oxadiazole into an acylhydrazide through a sequence of two hydrolytic steps. An identical cleavage pattern was also observed both in vitro using the purified HDAC6 enzyme as well as in cellular systems. By employing advanced quantum and molecular mechanics (QM/MM) and QM calculations, we elucidated the mechanistic details of the two hydrolytic steps to obtain a comprehensive mechanistic view of the double hydrolysis of the oxadiazole ring. This was achieved by fully characterizing the reaction coordinate, including identification of the structures of all intermediates and transition states, together with calculations of their respective activation (free) energies. In addition, we ruled out several (intuitively) competing pathways. The computed data (ΔG‡ ≈ 21 kcal·mol–1 for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the −CF3 or −CHF2 substituent on the oxadiazole ring, which is a prerequisite for hydrolysis to occur. Overall, our data provide compelling evidence that the oxadiazole warheads can be efficiently transformed within the active sites of target metallohydrolases to afford reaction products possessing distinct selectivity and inhibition profiles.
Open Access: Open access publication
License: (CC BY 4.0) Creative Commons Attribution 4.0(CC BY 4.0) Creative Commons Attribution 4.0
Journal Title: ACS chemical biology
Publisher: Soc.
Publisher Place: Washington, DC
Volume: 18
Issue: 7
Original Publication: 10.1021/acschembio.3c00212
Page Start: 1594
Page End: 1640
Appears in Collections:Open Access Publikationen der MLU

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