Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6)

0574532 - BTÚ 2024 RIV US eng J - Journal Article
Motlová, Lucia - Šnajdr, Ivan - Kutil, Zsofia - Andris, Erik - Ptáček, Jakub - Novotná, Adéla - Nováková, Zora - Havlínová, Barbora - Tueckmantel, W. - Dráberová, Helena - Majer, Pavel - Schutkowski, M. - Kozikowski, A. - Rulíšek, Lubomír - Bařinka, Cyril
Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6).
ACS Chemical Biology. Roč. 18, č. 7 (2023), s. 1594-1610. ISSN 1554-8929. E-ISSN 1554-8937
R&D Projects: GA ČR(CZ) GA21-31806S; GA ČR(CZ) GA23-05940S; GA MŠMT(CZ) LUAUS23247
Research Infrastructure: CIISB III - 90242; EATRIS-CZ IV - 90253
Institutional support: RVO:86652036 ; RVO:61388963
Keywords : BASIS-SETS * COSMO * ENERGY * REFINEMENT
OECD category: Biochemistry and molecular biology
Impact factor: 4, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acschembio.3c00212

Histone deacetylase (HDAC) inhibitors used in the clinictypicallycontain a hydroxamate zinc-binding group (ZBG). However, more recentwork has shown that the use of alternative ZBGs, and, in particular,the heterocyclic oxadiazoles, can confer higher isoenzyme selectivityand more favorable ADMET profiles. Herein, we report on the synthesisand biochemical, crystallographic, and computational characterizationof a series of oxadiazole-based inhibitors selectively targeting theHDAC6 isoform. Surprisingly, but in line with a very recent findingreported in the literature, a crystal structure of the HDAC6/inhibitorcomplex revealed that hydrolysis of the oxadiazole ring transformsthe parent oxadiazole into an acylhydrazide through a sequence oftwo hydrolytic steps. An identical cleavage pattern was also observedboth in vitro using the purified HDAC6 enzyme aswell as in cellular systems. By employing advanced quantum and molecularmechanics (QM/MM) and QM calculations, we elucidated the mechanisticdetails of the two hydrolytic steps to obtain a comprehensive mechanisticview of the double hydrolysis of the oxadiazole ring. This was achievedby fully characterizing the reaction coordinate, including identificationof the structures of all intermediates and transition states, togetherwith calculations of their respective activation (free) energies.In addition, we ruled out several (intuitively) competing pathways.The computed data (& UDelta,G (& DDAG) & AP,21 kcal & BULL,mol(-1) for the rate-determining stepof the overall dual hydrolysis) are in very good agreement with theexperimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively)explain the role of theCF3 orCHF2 substituent on the oxadiazole ring, which is a prerequisitefor hydrolysis to occur. Overall, our data provide compelling evidencethat the oxadiazole warheads can be efficiently transformed withinthe active sites of target metallohydrolases to afford reaction productspossessing distinct selectivity and inhibition profiles.
Permanent Link: https://hdl.handle.net/11104/0347139