8BJK
X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor CPD11352
Summary for 8BJK
| Entry DOI | 10.2210/pdb8bjk/pdb |
| Descriptor | Histone deacetylase 6, ZINC ION, POTASSIUM ION, ... (5 entities in total) |
| Functional Keywords | histone deacetylase, deacetylation, inhibitor, danio rerio, hydrolase |
| Biological source | Danio rerio (zebrafish) |
| Total number of polymer chains | 1 |
| Total formula weight | 40397.54 |
| Authors | |
| Primary citation | Motlova, L.,Snajdr, I.,Kutil, Z.,Andris, E.,Ptacek, J.,Novotna, A.,Novakova, Z.,Havlinova, B.,Tueckmantel, W.,Draberova, H.,Majer, P.,Schutkowski, M.,Kozikowski, A.,Rulisek, L.,Barinka, C. Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6). Acs Chem.Biol., 18:1594-1610, 2023 Cited by PubMed 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 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 (Δ ≈ 21 kcal·mol for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the -CF or -CHF 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. PubMed: 37392419DOI: 10.1021/acschembio.3c00212 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.35 Å) |
Structure validation
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