Aza-SAHA Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout.

We report the first well-characterized selective chemical probe for histone deacetylase 10 (HDAC10) with unprecedented selectivity over other HDAC isozymes. HDAC10 deacetylates polyamines and has a distinct substrate specificity, making it unique among the 11 zinc-dependent HDAC hydrolases. Taking inspiration from HDAC10 polyamine substrates, we systematically inserted an amino group ("aza-scan") into the hexyl linker moiety of the approved drug Vorinostat (SAHA). This one-atom replacement (C→N) transformed SAHA from an unselective pan-HDAC inhibitor into a specific HDAC10 inhibitor. Optimization of the aza-SAHA structure yielded the HDAC10 chemical probe DKFZ-748, with potency and selectivity demonstrated by cellular and biochemical target engagement, as well as thermal shift assays. Cocrystal structures of our aza-SAHA derivatives with HDAC10 provide a structural rationale for potency, and chemoproteomic profiling confirmed exquisite cellular HDAC10-selectivity of DKFZ-748 across the target landscape of HDAC drugs. Treatment of cells with DKFZ-748, followed by quantification of selected polyamines, validated for the first time the suspected cellular function of HDAC10 as a polyamine deacetylase. Finally, in a polyamine-limiting in vitro tumor model, DKFZ-748 showed dose-dependent growth inhibition of HeLa cells. We expect DKFZ-748 and related probes to enable further studies on the enigmatic biology of HDAC10 and acetylated polyamines in both physiological and pathological settings.

First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement.

Histone deacetylases (HDACs) are important epigenetic regulators involved in many diseases, especially cancer. Five HDAC inhibitors have been approved for anticancer therapy and many are in clinical trials. Among the 11 zinc-dependent HDACs, HDAC10 has received relatively little attention by drug discovery campaigns, despite its involvement, e. g., in the pathogenesis of neuroblastoma. This is due in part to a lack of robust enzymatic conversion assays. In contrast to the protein lysine deacetylase and deacylase activity of most other HDAC subtypes, it has recently been shown that HDAC10 has strong preferences for deacetylation of oligoamine substrates like acetyl-putrescine or -spermidine. Hence, it is also termed a polyamine deacetylase (PDAC). Here, we present the first fluorescent enzymatic conversion assay for HDAC10 using an aminocoumarin-labelled acetyl-spermidine derivative to measure its PDAC activity, which is suitable for high-throughput screening. Using this assay, we identified potent inhibitors of HDAC10-mediated spermidine deacetylation in vitro. Based on the oligoamine preference of HDAC10, we also designed inhibitors with a basic moiety in appropriate distance to the zinc binding hydroxamate that showed potent inhibition of HDAC10 with high selectivity, and we solved a HDAC10-inhibitor structure using X-ray crystallography. We could demonstrate selective cellular target engagement for HDAC10 but a lysosomal phenotype in neuroblastoma cells that was previously associated with HDAC10 inhibition was not observed. Thus, we have developed new chemical probes for HDAC10 that allow further clarification of the biological role of this enzyme.

X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10.

Histone deacetylase 10 (HDAC10) is a zinc-dependent polyamine deacetylase enriched in the cytosol of eukaryotic cells. The active site of HDAC10 contains catalytic residues conserved in other HDAC isozymes that function as lysine deacetylases: Y307 assists the zinc ion in polarizing the substrate carbonyl for nucleophilic attack, and the H136-H137 dyad serves general base-general acid functions. As an inducer of autophagy, HDAC10 is an attractive target for the design of selective inhibitors that may be useful in cancer chemotherapy. Because detailed structural information regarding the catalytic mechanism of HDAC10 may inform new approaches to inhibitor design, we now report X-ray crystal structures of HDAC10 in which reaction intermediates with substrates N8-acetylspermidine and N-acetylputrescine are trapped in the active site. The Y307F substitution prevents activation of the substrate carbonyl for nucleophilic attack by the zinc-bound water molecule, thereby enabling crystallographic isolation of intact enzyme-substrate complexes. The H137A substitution removes the catalytically obligatory general acid, thereby enabling crystallographic isolation of oxyanionic tetrahedral intermediates. Finally, the acetate complex with the wild-type enzyme represents a product complex after dissociation of the polyamine coproduct. Taken together, these structures provide snapshots of the reaction coordinate of acetylpolyamine hydrolysis and are consistent with a mechanism in which tandem histidine residues H136 and H137 serve as general base and general acid catalysts, respectively. The function of the histidine dyad in the HDAC10 mechanism appears to be similar to that in HDAC6, but not HDAC8 in which both functions are served by the second histidine of the tandem pair.

Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation.

Eukaryotic histone deacetylase 10 (HDAC10) is a Zn2+-dependent hydrolase that exhibits catalytic specificity for the hydrolysis of the polyamine N8-acetylspermidine. The recently determined crystal structure of HDAC10 from Danio rerio (zebrafish) reveals a narrow active site cleft and a negatively charged "gatekeeper" (E274) that favors the binding of the slender cationic substrate. Because HDAC10 expression is upregulated in advanced-stage neuroblastoma and induces autophagy, the selective inhibition of HDAC10 suppresses the autophagic response and renders cancer cells more susceptible to cytotoxic chemotherapeutic drugs. Here, we describe X-ray crystal structures of zebrafish HDAC10 complexed with eight different analogues of N8-acetylspermidine. These analogues contain different Zn2+-binding groups, such as hydroxamate, thiolate, and the tetrahedral gem-diolate resulting from the addition of a Zn2+-bound water molecule to a ketone carbonyl group. Notably, the chemistry that accompanies the binding of ketonic substrate analogues is identical to the chemistry involved in the first step of catalysis, i.e., nucleophilic attack of a Zn2+-bound water molecule at the scissile carbonyl group of N8-acetylspermidine. The most potent inhibitor studied contains a thiolate Zn2+-binding group. These structures reveal interesting geometric changes in the metal coordination polyhedron that accommodate inhibitor binding. Additional interactions in the active site highlight features contributing to substrate specificity. These interactions are likely to contribute to inhibitor binding selectivity and will inform the future design of compounds selective for HDAC10 inhibition.

Studies of the pathways open to copper water oxidation catalysts containing proximal hydroxy groups during basic electrocatalysis.

Water oxidation can lead to a sustainable source of energy, but for water oxidation catalysts to be economical they must use earth abundant metals. We report here 2:1 6,6'-dihydroxybipyridine (6,6'-dhbp)/copper complexes that are capable of electrocatalytic water oxidation in aqueous base (pH = 10-14). Two crystal structures of the complex that contains 6,6'-dhbp and copper(II) in a ratio of 2:1 (complex 1) are presented at different protonation states. The thermodynamic acid dissociation constants were measured for complex 1, and these show that the complex is fully deprotonated above pH = 8.3 (i.e., under water oxidation conditions). CW-EPR, ENDOR, and HYSCORE spectroscopy confirmed that the 6,6'-dhbp ligand is bound to the copper ion over a wide pH range which shows how pH influences precatalyst structure. Additional copper(II) complexes were synthesized from the ligands 4,4'-dhbp (complex 2) and 6,6'-dimethoxybipyridine (complexes 3 and 4). A zinc complex of 6,6'-dhbp was also synthesized (complex 5). Crystal structures are reported for 1 (in two protonation states), 3, 4, and 5. Water oxidation studies using several of the above compounds (1, 2, 4, and 5) at pH = 12.6 have illustrated that both copper and proximal OH groups are necessary for water oxidation at a low overpotential. Our most active catalyst 1 was found to have an overpotential of 477 mV for water oxidation at a moderate rate of kcat = 0.356 s(-1) with a competing irreversible oxidation event at a rate of 1.082 s(-1). Furthermore, our combined work supports previous observations in which OH/O(-) groups on the bipyridine rings can hydrogen bond with metal bound substrate, support unusual binding modes, and potentially facilitate proton coupled electron transfer.

Iridium dihydroxybipyridine complexes show that ligand deprotonation dramatically speeds rates of catalytic water oxidation.

We report highly active iridium precatalysts, [Cp*Ir(N,N)Cl]Cl (1-4), for water oxidation that are supported by recently designed dihydroxybipyridine (dhbp) ligands. These ligands can readily be deprotonated in situ to alter the electronic properties at the metal; thus, these catalyst precursors have switchable properties that are pH-dependent. The pKa values in water of the iridium complexes are 4.6(1) and 4.4(2) with (N,N) = 6,6'-dhbp and 4,4'-dhbp, respectively, as measured by UV-vis spectroscopy. For homogeneous water oxidation catalysis, the sacrificial oxidant NaIO4 was found to be superior (relative to CAN) and allowed for catalysis to occur at higher pH values. With NaIO4 as the oxidant at pH 5.6, water oxidation occurred most rapidly with (N,N) = 4,4'-dhbp, and activity decreased in the order 4,4'-dhbp (3) > 6,6'-dhbp (2) ≫ 4,4'-dimethoxybipyridine (4) > bipy (1). Furthermore, initial rate studies at pH 3-6 showed that the rate enhancement with dhbp complexes at high pH is due to ligand deprotonation rather than the pH alone accelerating water oxidation. Thus, the protic groups in dhbp improve the catalytic activity by tuning the complexes' electronic properties upon deprotonation. Mechanistic studies show that the rate law is first-order in an iridium precatalyst, and dynamic light scattering studies indicate that catalysis appears to be homogeneous. It appears that a higher pH facilitates oxidation of precatalysts 2 and 3 and their [B(Ar(F))4](-) salt analogues 5 and 6. Both 2 and 5 were crystallographically characterized.

Identification of histone deacetylase 10 (HDAC10) inhibitors that modulate autophagy in transformed cells.

Histone deacetylases (HDACs) are a family of 18 epigenetic modifiers that fall into 4 classes. Histone deacetylase inhibitors (HDACi) are valid tools to assess HDAC functions. HDAC6 and HDAC10 belong to the class IIb subgroup of the HDAC family. The targets and biological functions of HDAC10 are ill-defined. This lack of knowledge is due to a lack of specific and potent HDAC10 inhibitors with cellular activity. Here, we have synthesized and characterized piperidine-4-acrylhydroxamates as potent and highly selective inhibitors of HDAC10. This was achieved by targeting the acidic gatekeeper residue Glu274 of HDAC10 with a basic piperidine moiety that mimics the interaction of the polyamine substrate of HDAC10. We have confirmed the binding modes of selected inhibitors using X-ray crystallography. Promising candidates were selected based on their specificity by in vitro profiling using recombinant HDACs. The most promising HDAC10 inhibitors 10c and 13b were tested for specificity in acute myeloid leukemia (AML) cells with the FLT3-ITD oncogene. By immunoblot experiments we assessed the hyperacetylation of histones and tubulin-α, which are class I and HDAC6 substrates, respectively. As validated test for HDAC10 inhibition we used flow cytometry assessing autolysosome formation in neuroblastoma and AML cells. We demonstrate that 10c and 13b inhibit HDAC10 with high specificity over HDAC6 and with no significant impact on class I HDACs. The accumulation of autolysosomes is not a consequence of apoptosis and 10c and 13b are not toxic for normal human kidney cells. These data show that 10c and 13b are nanomolar inhibitors of HDAC10 with high specificity. Thus, our new HDAC10 inhibitors are tools to identify the downstream targets and functions of HDAC10 in cells.

Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase.

The cytosolic class IIb histone deacetylase HDAC10 is an emerging target for drug design. As an inducer of autophagy, its selective inhibition suppresses the autophagic response that otherwise attenuates the efficacy of cytotoxic cancer chemotherapy drugs. HDAC10 is a zinc-dependent polyamine deacetylase exhibiting maximal catalytic activity against N8-acetylspermidine. As revealed in the structure of Danio rerio (zebrafish) HDAC10, two conserved structural motifs direct this narrow substrate specificity: a 310 helix containing the P(E,A)CE motif that sterically constricts the active site and an electrostatic "gatekeeper," E274, that confers selectivity for cationic polyamine substrates. To accelerate drug design efforts targeting human HDAC10, we now report the preparation of "humanized" zebrafish HDAC10 in which two amino acid substitutions, A24E and D94A, yield an active site contour more similar to that of human HDAC10. X-ray crystal structures of this HDAC10 variant complexed with Tubastatin A and indole analogues bearing pendant tertiary amines reveal that inhibitors capable of hydrogen bonding with gatekeeper E274 exhibit high affinity and selectivity for HDAC10 over HDAC6 (the other class IIb isozyme). Moreover, these structures reveal that the P(E,A)CE motif helix can shift by up to 2 Å to accommodate the binding of bulky inhibitors. Thus, slender polyamine-like inhibitor structures are not exclusively required for selective, high affinity binding to HDAC10. Indeed, the flexibility of the P(E,A)CE motif helix could conceivably enable the binding of certain protein substrates.

Discovery of the cryptic function of terpene cyclases as aromatic prenyltransferases.

Catalytic versatility is an inherent property of many enzymes. In nature, terpene cyclases comprise the foundation of molecular biodiversity as they generate diverse hydrocarbon scaffolds found in thousands of terpenoid natural products. Here, we report that the catalytic activity of the terpene cyclases AaTPS and FgGS can be switched from cyclase to aromatic prenyltransferase at basic pH to generate prenylindoles. The crystal structures of AaTPS and FgGS provide insights into the catalytic mechanism of this cryptic function. Moreover, aromatic prenyltransferase activity discovered in other terpene cyclases indicates that this cryptic function is broadly conserved among the greater family of terpene cyclases. We suggest that this cryptic function is chemoprotective for the cell by regulating isoprenoid diphosphate concentrations so that they are maintained below toxic thresholds.

Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors.

We report the synthesis and evaluation of a class of selective multitarget agents for the inhibition of HDAC6, HDAC8, and HDAC10. The concept for this study grew out of a structural analysis of the two selective inhibitors Tubastatin A (HDAC6/10) and PCI-34051 (HDAC8), which we recognized share the same N-benzylindole core. Hybridization of the two inhibitor structures resulted in dihydroxamic acids with benzyl-indole and -indazole core motifs. These substances exhibit potent activity against HDAC6, HDAC8, and HDAC10, while retaining selectivity over HDAC1, HDAC2, and HDAC3. The best substance inhibited the viability of the SK-N-BE(2)C neuroblastoma cell line with an IC50 value similar to a combination treatment with Tubastatin A and PCI-34051. This compound class establishes a proof of concept for such hybrid molecules and could serve as a starting point for the further development of enhanced HDAC6/8/10 inhibitors.

Crystal structures of sodium-, lithium-, and ammonium 4,5-di-hydroxy-benzene-1,3-di-sulfonate (tiron) hydrates.

The solid-state structures of the Na+, Li+, and NH4+ salts of the 4,5-di-hydroxy-benzene-1,3-di-sulfonate (tiron) dianion are reported, namely disodium 4,5-di-hydroxy-benzene-1,3-di-sulfonate, 2Na+·C6H4O8S22-, µ-4,5-di-hydroxy-benzene-1,3-di-sulfonato-bis-[aqua-lithium(I)] hemihydrate, [Li2(C6H4O8S2)(H2O)2]·0.5H2O, and di-ammonium 4,5-di-hydroxy-benzene-1,3-di-sulfonate monohydrate, 2NH4+·C6H4O8S22-·H2O. Inter-molecular inter-actions vary with the size of the cation, and the asymmetric unit cell, and the macromolecular features are also affected. The sodium in Na2(tiron) is coordinated in a distorted octa-hedral environment through the sulfonate oxygen and hydroxyl oxygen donors on tiron, as well as an inter-stitial water mol-ecule. Lithium, with its smaller ionic radius, is coordinated in a distorted tetra-hedral environment by sulfonic and phenolic O atoms, as well as water in Li2(tiron). The surrounding tiron anions coordinating to sodium or lithium in Na2(tiron) and Li2(tiron), respectively, result in a three-dimensional network held together by the coordinate bonds to the alkali metal cations. The formation of such a three-dimensional network for tiron salts is relatively rare and has not been observed with monovalent cations. Finally, (NH4)2(tiron) exhibits extensive hydrogen-bonding arrays between NH4+ and the surrounding tiron anions and inter-stitial water mol-ecules. This series of structures may be valuable for understanding charge transfer in a putative solid-state fuel cell utilizing tiron.

Crystal structures of bis- and hexakis[(6,6'-di-hydroxy-bipyridine)copper(II)] nitrate coordination complexes.

Two multinuclear complexes synthesized from Cu(NO3)2 and 6,6'-di-hydroxy-bipyridine (dhbp) exhibit bridging nitrate and hydroxide ligands. The dinuclear complex (6,6'-di-hydroxy-bipyridine-2κ(2) N,N')[µ-6-(6-hy-droxy-pyridin-2-yl)pyridin-2-olato-1:2κ(3) N,N':O (2)](µ-hydroxido-1:2κ(2) O:O')(µ-nitrato-1:2κ(2) O:O')(nitrato-1κO)dicopper(II), [Cu2(C10H7N2O2)(OH)(NO3)2(C10H8N2O2)] or [Cu(6-OH-6'-O-bpy)(NO3)(µ-OH)(µ-NO3)Cu(6,6'-dhbp)], (I), with a 2:1 ratio of nitrate to hydroxide anions and one partially deprotonated dhbp ligand, forms from a water-ethanol mixture at neutral pH. The hexa-nuclear complex bis-(µ3-bi-pyridine-2,2'-diolato-κ(3) O:N,N':O')tetra-kis-(6,6'-di-hydroxy-bipyridine-κ(2) N,N')tetra-kis-(µ-hydroxido-κ(2) O:O')bis-(methanol-κO)tetra-kis-(µ-nitrato-κ(2) O:O')hexa-copper(II), [Cu6(C10H6N2O2)2(CH4O)2(OH)4(NO3)4(C10H8N2O2)4] or [Cu(6,6'-dhbp)(µ-NO3)2(µ-OH)Cu(6,6'-O-bpy)(µ-OH)Cu(6,6'dhbp)(CH3OH)]2, (II), with a 1:1 NO3-OH ratio and two fully protonated and fully deprotonated dhbp ligands, was obtained by methanol recrystallization of material obtained at pH 3. Complex (II) lies across an inversion center. Complexes (I) and (II) both display intra-molecular O-H⋯O hydrogen bonding. Inter-molecular O-H⋯O hydrogen bonding links symmetry-related mol-ecules forming chains along [100] for complex (I) with π-stacking along [010] and [001]. Complex (II) forms inter-molecular O-H⋯O hydrogen-bonded chains along [010] with π-stacking along [100] and [001].