Hydroxamic Acids Immobilized on Resins (HAIRs): Synthesis of Dual-Targeting HDAC Inhibitors and HDAC Degraders (PROTACs).

Inhibition of more than one cancer-related pathway by multi-target agents is an emerging approach in modern anticancer drug discovery. Here, based on the well-established synergy between histone deacetylase inhibitors (HDACi) and alkylating agents, we present the discovery of a series of alkylating HDACi using a pharmacophore-linking strategy. For the parallel synthesis of the target compounds, we developed an efficient solid-phase-supported protocol using hydroxamic acids immobilized on resins (HAIRs) as stable and versatile building blocks for the preparation of functionalized HDACi. The most promising compound, 3 n, was significantly more active in apoptosis induction, activation of caspase 3/7, and formation of DNA damage (γ-H2AX) than the sum of the activities of either active principle alone. Furthermore, to demonstrate the utility of our preloaded resins, the HAIR approach was successfully extended to the synthesis of a proof-of-concept proteolysis-targeting chimera (PROTAC), which efficiently degrades histone deacetylases.

Preferential HDAC6 inhibitors derived from HPOB exhibit synergistic antileukemia activity in combination with decitabine.

Histone deacetylase 6 (HDAC6) is an emerging drug target to treat oncological and non-oncological conditions. Since highly selective HDAC6 inhibitors display limited anticancer activity when used as single agent, they usually require combination therapies with other chemotherapeutics. In this work, we synthesized a mini library of analogues of the preferential HDAC6 inhibitor HPOB in only two steps via an Ugi four-component reaction as the key step. Biochemical HDAC inhibition and cell viability assays led to the identification of 1g (highest antileukemic activity) and 2b (highest HDAC6 inhibition) as hit compounds. In subsequent combination screens, both 1g and especially 2b showed synergy with DNA methyltransferase inhibitor decitabine in acute myeloid leukemia (AML). Our findings highlight the potential of combining HDAC6 inhibitors with DNA methyltransferase inhibitors as a strategy to improve AML treatment outcomes.

On the physical origin of the cation-anion intermediate bond in ionic liquids Part I. Placing a (weak) hydrogen bond between two charges.

The intermediate bond forces in ionic liquids are investigated from static quantum chemical calculations at various methods and two basis sets. The experimentally observed red-shift of the donor-proton bond stretching frequency due to a bond elongation is confirmed by all methods. Comparing Hartree-Fock to second-order Møller-Plesset perturbation theory, the Hartree-Fock method gives in many cases an erroneous description of the geometries. Furthermore, the Hartree-Fock interaction energies can deviate up to 60 kJ mol(-1) from Møller-Plesset perturbation theory indicating the importance of dispersion interaction. While the usual trends of decreasing stability or interaction energies with increasing ion sizes are found, the geometries involving hydrogen atoms do not change this order of total interaction energies. Therefore, the hydrogen bond is not the most important interaction for ion pairs with regard to the total interaction energy. On the other hand, the different established analysis methods give rise to hydrogen bonding in several ion pairs. Charge analysis reveals the hydrogen-bonding character of the ion pair and shows, depending on the type of ions combined and further on the type of conformers considered, that a hydrogen bond can be present. The possibility of hydrogen bonding is also shown by an analysis of the frontier orbitals. Calculating potential energy surfaces and observing from this the change in the donor proton bond indicates that regular hydrogen bonds are possible in ion pairs of ionic liquids. Thereby, the maximum of bond elongation exceeds the one of a usual hydrogen bond by far. The more salt-like hydrogen-bonded ion pair [NH(4)][BF(4)] exhibits a steeper maximum than the more ionic liquid like ion pair [EtNH(3)][BF(4)]. The fact that imidazolium-based ionic liquids as [Emim][Cl] can display two faces, hydrogen bonding and purely ionic bonding, points to a disturbing rather than stabilizing role of hydrogen bonding on the interaction of the counterions in imidazolium-based ionic liquids. While geometry and charge analysis provides attributes of weak (blue-shifted) hydrogen bonds, large bond elongations accompanied by red-shifts are obtained for the ion pairs investigated. This can be understood by the simple fact that these imidazolium-based ionic liquid ion pairs constitute weak hydrogen bonds placed between two delocalized charges.

Structure-Based Screening of Tetrazolylhydrazide Inhibitors versus KDM4 Histone Demethylases.

Human histone demethylases are known to play an important role in the development of several tumor types. Consequently, they have emerged as important medical targets for the treatment of human cancer. Herein, structural studies on tetrazolylhydrazide inhibitors as a new scaffold for a certain class of histone demethylases, the JmjC proteins, are reported. A series of compounds are structurally described and their respective binding modes to the KDM4D protein, which serves as a high-resolution model to represent the KDM4 subfamily in crystallographic studies, are examined. Similar to previously reported inhibitors, the compounds described herein are competitors for the natural KDM4 cofactor, 2-oxoglutarate. The tetrazolylhydrazide scaffold fills an important gap in KDM4 inhibition and newly described, detailed interactions of inhibitor moieties pave the way to the development of compounds with high target-binding affinity and increased membrane permeability, at the same time.

The Clinically Used Iron Chelator Deferasirox Is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases.

Fe(II)- and 2-oxoglutarate (2OG)-dependent JumonjiC domain-containing histone demethylases (JmjC KDMs) are "epigenetic eraser" enzymes involved in the regulation of gene expression and are emerging drug targets in oncology. We screened a set of clinically used iron chelators and report that they potently inhibit JMJD2A (KDM4A) in vitro. Mode of action investigations revealed that one compound, deferasirox, is a bona fide active site-binding inhibitor as shown by kinetic and spectroscopic studies. Synthesis of derivatives with improved cell permeability resulted in significant upregulation of histone trimethylation and potent cancer cell growth inhibition. Deferasirox was also found to inhibit human 2OG-dependent hypoxia inducible factor prolyl hydroxylase activity. Therapeutic effects of clinically used deferasirox may thus involve transcriptional regulation through 2OG oxygenase inhibition. Deferasirox might provide a useful starting point for the development of novel anticancer drugs targeting 2OG oxygenases and a valuable tool compound for investigations of KDM function.

Development of Erasin: a chromone-based STAT3 inhibitor which induces apoptosis in Erlotinib-resistant lung cancer cells.

Inhibition of protein-protein interactions by small molecules offers tremendous opportunities for basic research and drug development. One of the fundamental challenges of this research field is the broad lack of available lead structures from nature. Here, we demonstrate that modifications of a chromone-based inhibitor of the Src homology 2 (SH2) domain of the transcription factor STAT5 confer inhibitory activity against STAT3. The binding mode of the most potent STAT3 inhibitor Erasin was analyzed by the investigation of structure-activity relationships, which was facilitated by chemical synthesis and biochemical activity analysis, in combination with molecular docking studies. Erasin inhibits tyrosine phosphorylation of STAT3 with selectivity over STAT5 and STAT1 in cell-based assays, and increases the apoptotic rate of cultured NSCLC cells in a STAT3-dependent manner. This ability of Erasin also extends to HCC-827 cells with acquired resistance against Erlotinib, a clinically used inhibitor of the EGF receptor. Our work validates chromone-based acylhydrazones as privileged structures for antagonizing STAT SH2 domains, and demonstrates that apoptosis can be induced in NSCLC cells with acquired Erlotinib resistance by direct inhibition of STAT3.

4-Biphenylalanine- and 3-Phenyltyrosine-Derived Hydroxamic Acids as Inhibitors of the JumonjiC-Domain-Containing Histone Demethylase KDM4A.

Overexpression of the histone lysine demethylase KDM4A, which regulates H3K9 and H3K36 methylation states, has been related to the pathology of several human cancers. We found that a previously reported hydroxamate-based histone deacetylase (HDAC) inhibitor (SW55) was also able to weakly inhibit this demethylase with an IC50 value of 25.4 µm. Herein we report the synthesis and biochemical evaluations, with two orthogonal in vitro assays, of a series of derivatives of this lead structure. With extensive chemical modifications on the lead structure, also by exploiting the versatility of the radical arylation with aryldiazonium salts, we were able to increase the potency of the derivatives against KDM4A to the low-micromolar range and, more importantly, to obtain demethylase selectivity with respect to HDACs. Cell-permeable derivatives clearly showed a demethylase-inhibition-dependent antiproliferative effect against HL-60 human promyelocytic leukemia cells.

Substituted 2-(2-aminopyrimidin-4-yl)pyridine-4-carboxylates as potent inhibitors of JumonjiC domain-containing histone demethylases.

BACKGROUND: Aberrant expression of iron(II)- and 2-oxoglutarate-dependent JumonjiC histone demethylases has been linked to cancer. Potent demethylase inhibitors are drug candidates and biochemical tools to elucidate the functional impact of demethylase inhibition. METHODS & RESULTS: Virtual screening identified a novel lead scaffold against JMJD2A with low-micromolar potency in vitro. Analogs were acquired from commercial sources respectively synthesized in feedback with biological testing. Optimized compounds were transformed into cell-permeable prodrugs. A cocrystal x-ray structure revealed the mode of binding of these compounds as competitive to 2-oxoglutarate and confirmed kinetic experiments. Selectivity studies revealed a preference for JMJD2A and JARID1A over JMJD3. CONCLUSION: Virtual screening and rational structural optimization led to a novel scaffold for highly potent and selective JMJD2A inhibitors.

Tetrazolylhydrazides as Selective Fragment-Like Inhibitors of the JumonjiC-Domain-Containing Histone Demethylase KDM4A.

The JumonjiC-domain-containing histone demethylase 2A (JMJD2A, KDM4A) is a key player in the epigenetic regulation of gene expression. Previous publications have shown that both elevated and lowered enzyme levels are associated with certain types of cancer, and therefore the definite role of KDM4A in oncogenesis remains elusive. To identify a novel molecular starting point with favorable physicochemical properties for the investigation of the physiological role of KDM4A, we screened a number of molecules bearing an iron-chelating moiety by using two independent assays. In this way, we were able to identify 2-(1H-tetrazol-5-yl)acetohydrazide as a novel fragment-like lead structure with low relative molecular mass (Mr =142 Da), low complexity, and an IC50 value of 46.6 µm in a formaldehyde dehydrogenase (FDH)-coupled assay and 2.4 µm in an antibody-based assay. Despite its small size, relative selectivity against two other demethylases could be demonstrated for this compound. This is the first example of a tetrazole group as a warhead in JMJD demethylases.

The role of histone demethylases in cancer therapy.

Reversible histone methylation has emerged in the last few years as an important mechanism of epigenetic regulation. Histone methyltransferases and demethylases have been identified as contributing factors in the development of several diseases, especially cancer. Therefore, they have been postulated to be new drug targets with high therapeutic potential. Here, we review histone demethylases with a special focus on their potential role in oncology drug discovery. We present an overview over the different classes of enzymes, their biochemistry, selected data on their role in physiology and already available inhibitors.

Coupled Cluster in Condensed Phase. Part I: Static Quantum Chemical Calculations of Hydrogen Fluoride Clusters.

A multiscale approach with roots in electronic structure calculations relies on the good description of intermolecular forces. In this study we lay the foundations for a condensed phase treatment based on the electronic structure of hydrogen fluoride on a very high level of theory. This investigation comprises cluster calculations in a static quantum chemical approach employing density functional theory, second order Møller-Plesset perturbation theory (MP2) and the coupled cluster singles, doubles with perturbative triples method in combination with several basis sets as well as at the complete basis set limit. The clusters we considered are up to 12 monomer units large and consist of ring and chain structures. We find a good agreement of the intramolecular distance obtained from the MP2 approach and the largest basis set. The binding energy of the hydrogen fluoride dimer calculated from coupled cluster at the basis set limit agrees excellently with experiment, whereas the calculated frequencies at all levels agree reasonably well with different experimental values. Large cooperative effects are observed for the ring structures as compared to the chain clusters. The energy per monomer unit indicates the most stable structures to be the ring clusters.

Coupled Cluster in Condensed Phase. Part II: Liquid Hydrogen Fluoride from Quantum Cluster Equilibrium Theory.

Treating the bulk phase with high-level ab initio methods, such as coupled cluster, is a nontrivial task because of the computational costs of these electronic structure methods. In this part of our hydrogen fluoride study we make use of the quantum cluster equilibrium method, which employs electronic structure input of small clusters and combines it with simple statistical mechanics in order to describe condensed phase phenomena. If no parameter adjustment is applied, then the lower quantum chemical methods, such as density functional theory in conjunction with the generalized gradient approximation, provide wrong results in accordance with the description of the strength of the interaction in the clusters. While density functional theory describes the liquid phase too dense due to overbinding of the clusters, the coupled cluster method and the perturbation theory at the complete basis set limit agree well with experimental observations. If we allow the two parameters in the quantum cluster equilibrium method to vary, then these are able to compensate the overbinding, thereby leading to very good agreement with experiment. Correlated methods in combination with small basis sets giving rise to too weakly bound clusters cannot reach this accuracy even if the parameters are flexible. Only at the complete basis set limit, the performance of the correlated methods is again excellent.