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[Display omitted] PCI-34051 is a valuable tool to interrogate the therapeutic effects of selective inhibition of HDAC8. However, it has not advanced to clinical trials, perhaps due to poor PK or off-target effects. We hypothesized that the presence of a hydroxamic acid (HA) group in PCI-34051 contributed to its lack of advancement. Therefore, we replaced the HA in the PCI-34051 scaffold with a series of moieties that have the potential to bind to Zn and evaluated their activity in a HDAC8 assay. Surprisingly, none of the replacements effectively mimicked the HA, and analogs lost significant potency. Evaluation of the analogs' affinity to Zn indicated that none had affinity for Zn within the same range as the HA. These studies point to the difficulty in the application of bioisosteric replacements for Zn binding motifs. [ABSTRACT FROM AUTHOR]

N ′-Propylhydrazide analogs of hydroxamic inhibitors of histone deacetylases (HDACs), including tubastatin A, vorinostat and belinostat, were synthesized. All prepared compounds inhibited HDAC1/2/3, but not HDAC6, except for one hydrazide analog of HDAC4/5/7 inhibitor that was completely inactive. A novel 4-substituted derivative of N ′-propylbenzohydrazide with extremely high anti-HCV activity was discovered. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Twenty hydroxamic acid inhibitors of class IIa histone deacetylases were synthesized. • Inhibitor 22 (CHDI-390576) was selective over class I and IIb histone deacetylases. • Inhibitor 22 can reach high exposure levels in mouse plasma, muscle and brain. Abstract We have identified a potent, cell permeable and CNS penetrant class IIa histone deacetylase (HDAC) inhibitor 22 , with >500-fold selectivity over class I HDACs (1,2,3) and ∼150-fold selectivity over HDAC8 and the class IIb HDAC6 isoform. Dose escalation pharmacokinetic analysis demonstrated that upon oral administration, compound 22 can reach exposure levels in mouse plasma, muscle and brain in excess of cellular class IIa HDAC IC 50 levels for ∼8 h. Given the interest in aberrant class IIa HDAC function for a number of neurodegenerative, neuromuscular, cardiac and oncology indications, compound 22 (also known as CHDI-390576) provides a selective and potent compound to query the role of class IIa HDAC biology, and the impact of class IIa catalytic site occupancy in vitro and in vivo. [ABSTRACT FROM AUTHOR]

N -Hydroxy-2-arylisoindoline-4-carboxamides are potent and selective inhibitors of HDAC11. The discovery, synthesis, and structure activity relationships of this novel series of inhibitors are reported. An advanced analog ( FT895 ) displays promising cellular activity and pharmacokinetic properties that make it a useful tool to study the biology of HDAC11 and its potential use as a therapeutic target for oncology and inflammation indications. [ABSTRACT FROM AUTHOR]

Histone deacetylases (HDACs) play a pivotal role not only in gene expression but also in DNA repair. Herein, we report the successful design, synthesis and evaluation of a chlorambucil derivative named vorambucil with a hydroxamic acid tail as a DNA/HDAC dual-targeting inhibitor. Vorambucil obtained both potent DNA and HDACs inhibitory activities. Molecular docking results supported the initial pharmacophoric hypothesis and rationalized the potent inhibitory activity of vorambucil against HDAC1, HDAC2 and HDAC6. Vorambucil showed potent antiproliferative activity against all the test four cancer cell lines with IC 50 values of as low as 3.2–6.2 μM and exhibited 5.0–18.3-fold enhanced antiproliferative activity than chlorambucil. Vorambucil also significantly inhibits colony formation of A375 cancer cells. Further investigation showed that vorambucil remarkably induced apoptosis and arrested the cell cycle of A375 cells at G2/M phase. Vorambucil could be a promising candidate and a useful tool to elucidate the role of those DNA/HDAC dual-targeting inhibitors for cancer therapy. [ABSTRACT FROM AUTHOR]

The astacin proteases meprin α and β are emerging drug targets for treatment of disorders such as kidney failure, fibrosis or inflammatory bowel disease. However, there are only few inhibitors of both proteases reported to date. Starting from NNGH as lead structure, a detailed elaboration of the structure-activity relationship of meprin β inhibitors was performed, leading to compounds with activities in the lower nanomolar range. Considering the preference of meprin β for acidic residues in the P1′ position, the compounds were optimized. Acidic modifications induced potent inhibition and >100-fold selectivity over other structurally related metalloproteases such as MMP-2 or ADAM10. [ABSTRACT FROM AUTHOR]

The human parasite Plasmodium falciparum kills an estimated 445,000 people a year, with the most fatalities occurring in African children. Previous studies identified falcilysin (FLN) as a malarial metalloprotease essential for parasite development in the human host. Despite its essentiality, the biological roles of this protease are not well understood. Here we describe the optimization of a piperazine-based hydroxamic acid scaffold to develop the first reported inhibitors of FLN. Inhibitors were tested against cultured parasites, and parasiticidal activity correlated with potency against FLN. This suggests these compounds kill P. falciparum by blocking FLN, and that FLN is a druggable target. These compounds represent an important step towards validating FLN as a therapeutic target and towards the development of chemical tools to investigate the function of this protease. [ABSTRACT FROM AUTHOR]

[Display omitted] Thirteen 2-(N -(3-nitrophenyl)- N -phenylsulfonyl)aminoacetohydroxamic acids which were reported for the first time were designed and synthesized as novel urease inhibitors. Most of them showed higher potency than the positive control acetohydroxamic acid, with 2-(N -(3-nitrophenyl)- N -(4-bromophenylsulfonyl)aminoacetohydroxamic acid (d7) being the most active (IC 50 = 0.13 ± 0.01 μM). Compound d7 reversibly inhibits urease with mixed mechanism showing excellent binding affinity to urease active site (K D = 0.34 nM, K i =0.065 ± 0.003 µM and K i ′ = 1.20 ± 0.09 µM) and very low cytotoxicity against mammalian cells (cell viability of 91.4 % against HepG2 at 250 μg/mL). These positive results indicated that d7 may be used as the lead for further research to develop urease inhibitors with promising properties. [ABSTRACT FROM AUTHOR]

A series of pyridoxine hydroxamic acid analog bearing a 5- aryl -spacers were synthesized. Evaluation of these novel HIV integrase complex inhibitors revealed compounds with high potency against wild-type HIV virus. [ABSTRACT FROM AUTHOR]

A series of hybrids derived from 4-anilinoquinazoline and hydroxamic acid were designed, synthesized, and evaluated as dual inhibitors of vascular endothelia growth factor receptor-2 (VEGFR-2) tyrosine kinase and histone deacetylase (HDAC). Most of these compounds exhibited potent HDAC inhibition and moderate VEGFR-2 inhibition. Among them, compound 6l exhibited the most potent inhibitory activities against VEGFR-2 (IC 50 = 84 nM) and HDAC (IC 50 = 2.8 nM). It also showed the most potent antiproliferative ability against MCF-7, a human breast cancer line, with IC 50 of 1.2 μM. Docking simulation supported the initial pharmacophoric hypothesis and suggested a common mode of interaction of compound 6l at the active binding sites of VEGFR-2 and HDAC. [ABSTRACT FROM AUTHOR]

Tuberculosis (TB) continues to remain one of the most threatening diseases in the world. With the emergence of multi-drug resistant (MDR) and extensively drug resistant (XDR) strains, the need to develop new therapies is dire. The syntheses of a focused library of hydroxamates and hydroxamic acids is described, as well as anti-TB activity in the microplate alamar blue assay (MABA). A number of compounds exhibited good activity against Mtb , with notable compounds exhibiting MIC values in the range of 20–0.71 μM. This work suggests that both hydroxamates and their free acids may be incorporated into more complex scaffolds and serve as potential leads for the development of anti-TB agents. [ABSTRACT FROM AUTHOR]

Several salinomycin-hydroxamic acid conjugates were designed and synthesized. Most conjugates showed better antiproliferative activities than salinomycin in HT-29 colon cancer, HGC-27 gastric cancer, and especially in MDA-MB-231 triple-negative human breast cancer cells. These conjugates are stable in cell culture media, and they showed much better biological activities than the 1:1 physical mixture with hydroxamic acids and salinomycin. The better membrane permeability and hydrolysis rate of the conjugates may lead to the activity improvements. [ABSTRACT FROM AUTHOR]

Acyl derivatives of 4-(aminomethyl)- N -hydroxybenzamide are potent sub-type selective HDAC6 inhibitors. Constrained heterocyclic analogs based on 1,2,3,4-tetrahydropyrrolo[1,2- a ]pyrazine show further enhanced HDAC6 selectivity and inhibitory activity in cells. Homology models suggest that the heterocyclic spacer can more effectively access the wider catalytic channel of HDAC6 compared to other HDAC sub-types. [ABSTRACT FROM AUTHOR]

The synthesis and bio-evaluation of naturally occurring boswellic acids (BAs) as an alternate CAP for the design of new HDAC inhibitors is described. All the compounds were screened against a panel of human cancer cell lines to identify leads, which were subsequently examined for their potential to inhibit HDACs. The identified lead compound showed IC 50 value of 6 μm for HDACs, found to induce G 1 cell cycle arrest at significantly low concentration (1 μM) and caused significant loss in mitochondrial membrane potential at 5 and 10 μM. Furthermore, specific interactions of the lead molecule inside the catalytic domain were also studied through in silico molecular modeling. [ABSTRACT FROM AUTHOR]

[Display omitted] • First report comparing the enzymatic profile of three promising ZBGs of HDAC inhibitors. • Hydrazide-based HDAC inhibitors show slow-binding class I selective inhibitor with mixed binding mode. • The kinetics profile of benzamide is not only due to the ZBG, but also rely on the cap and linker groups. Hydroxamic acid and benzamide are the most commonly used zinc binding group (ZBG) for HDAC inhibitors both in clinic and pre-clinic. Recently, we discovered several analogs of new type HDAC inhibitors with hydrazide as ZBG. Representative compounds displayed high potency, class I HDAC selectivity and excellent pharmacokinetics profile. In this research, we synthesize tool compounds 4 and 6 by modifying the hydroxamic acid of SAHA with benzamide and hydrazide, respectively, and compare the potency, isoform selectivity, binding profile and enzymatic kinetics for the hydroxamate, benzamide and hydrazide-based inhibitors. It is well known that SAHA with hydroxamic acid is a pan-HDAC inhibitor with competitive binding and fast-on/fast-off profile. Compound 6 is a slow-binding class I selective inhibitor with mixed (competitive and non-competitive) binding mode, which is the same as the hydrazide inhibitors in our previous study. Compound 4 is a class I selective, fast-on/fast-off inhibitor with competitive binding mode to HDAC1/2/3, which is different with published benzamide MS275 and 106. Therefore, the kinetics profile of benzamide is not only due to the ZBG, but also rely on the cap and linker groups. To the best of our knowledge, this is the first report to compare the enzymatic profile of three promising ZBGs of HDAC inhibitors. [ABSTRACT FROM AUTHOR]

Abstract: A series of SAHA-like molecules were prepared introducing different lactam-carboxyamides in position 7 of the suberoylanilide skeleton. The activity against different HDAC isoforms was tested and the data compared with the corresponding linear products, without substituent in position 7. In general, this modification provided an effective reinforcement of in vitro activity. While the lactam size or the CO/NH group orientation did not strongly influence the inhibition, the contemporary modification of the suberoylamide fragment gave vary active variants in the lactam series, with compound 28 (ST8078AA1) that showed IC50 values between 2 and 10nM against all Class I HDAC isoforms, demonstrating it to be a large spectrum pan-inhibitor. This strong affinity with HDAC was also confirmed by the value of IC50 =0.5μM against H460 cells, ranking 28 as one of the most potent HDAC inhibitors described so far. [Copyright &y& Elsevier]

Abstract: A novel method for applying high-throughput docking to challenging metalloenzyme targets is described. The method utilizes information-based virtual transformation of library carboxylates to hydroxamic acids prior to docking, followed by compound acquisition, one-pot (two steps) chemical synthesis and in vitro screening. In two experiments targeting the botulinum neurotoxin serotype A metalloprotease light chain, hit rates of 32% and 18% were observed. [Copyright &y& Elsevier]

Abstract: We previously reported that caffeoyl-amino acidyl-hydroxamic acid (CA-Xaa-NHOH) acted as both a good antioxidant and tyrosinase inhibitor, in particular when caffeic acid was conjugated with proline or amino acids having aromatic ring like phenylalanine. Here, various hydroxycinnamic acid (HCA) derivatives were further conjugated with phenylalanyl hydroxamic acid and prolyl hydroxamic acid (HCA-Phe-NHOH and HCA-Pro-NHOH) to study the structure and activity relationship as both antioxidants and tyrosinase inhibitors. When their biological activities were evaluated, all HCA-Phe-NHOH and HCA-Pro-NHOH exhibited enhanced antioxidant activity compared to HCA alone. Moreover, derivatives of caffeic acid, ferulic acid, and sinapic acid inhibited lipid peroxidation more efficiently than vitamin E analogue (Trolox). In addition, derivatives of caffeic acid and sinapic acid efficiently inhibited tyrosinase activity and reduced melanin content in melanocytes Mel-Ab cell. [Copyright &y& Elsevier]

Abstract: The synthesis and antibacterial activity of heterocyclic methylsulfone hydroxamates is presented. Compounds in this series are potent inhibitors of the LpxC enzyme, a key enzyme involved in the production of lipopolysaccharide (LPS) found in the outer membrane of Gram-negative bacteria. SAR evaluation of compounds in this series revealed analogs with potent antibacterial activity against challenging Gram-negative species such as Pseudomonas aeruginosa and Klebsiella pneumoniae. [Copyright &y& Elsevier]

Abstract: Two different series of naphthalene and anthracene based hydroxamic acids having amino acid derivatives were synthesized. Single strand DNA cleavage was achieved on irradiation of newly synthesized hydroxamic acids by UV light (⩾350nm). Both reactive oxygen species (ROS) and generated radicals from hydroxamic acids were shown to be responsible for the DNA cleavage. Further, DNA cleaving ability of hydroxamic acids was found to be dependent on its concentration and on its structure. [Copyright &y& Elsevier]

Abstract: Lipid A is an essential component of the Gram negative outer membrane, which protects the bacterium from attack of many antibiotics. The Lipid A biosynthesis pathway is essential for Gram negative bacterial growth and is unique to these bacteria. The first committed step in Lipid A biosynthesis is catalysis by LpxC, a zinc dependent deacetylase. We show the design of an LpxC inhibitor utilizing a robust model which directed efficient design of picomolar inhibitors. Analysis of physiochemical properties drove design to focus on an optimal lipophilicity profile. Further structure based design took advantage of a conserved water network over the active site, and with the optimal lipophilicity profile, led to an improved LpxC inhibitor with in vivo activity against wild type Pseudomonas aeruginosa. [Copyright &y& Elsevier]

Abstract: Anti-aging and depigmentation have both been an important subject of study for skin disease and the cosmetic industry. Caffeic acid (CA) has shown synergistically enhanced antioxidant activity when conjugated with amino acids. Hydroxamic acid (NHOH) is a well-known metal chelator, potentially having both tyrosinase inhibitory activity and free radical scavenging activity. We prepared caffeoyl-amino acidyl-hydroxamic acid (CA-Xaa-NHOH) and found that caffeoyl-prolyl-hydroxamic acid (CA-Pro-NHOH) contained excellent antioxidant activity and tyrosinase inhibitory activity by various bioassay systems. Also, CA-Pro-NHOH showed mild melanogenesis inhibitory activity in Mel-Ab cells. [Copyright &y& Elsevier]

Abstract: We have developed an efficient method for synthesizing candidate histone deacetylase (HDAC) inhibitors in 96-well plates, which are used directly in high-throughput screening. We selected building blocks having hydrazide, aldehyde and hydroxamic acid functionalities. The hydrazides were coupled with different aldehydes in DMSO. The resulting products have the previously identified ‘cap/linker/biasing element’ structure known to favor inhibition of HDACs. These compounds were assayed without further purification. HDAC8-selective inhibitors were discovered from this novel collection of compounds. [Copyright &y& Elsevier]

Abstract: Aromatic analogues of the 2-oxoglutarate co-substrate of the hypoxia-inducible factor hydroxylases are shown to bind at the active site iron: Pyridine-2,4-dicarboxylate binds as anticipated with a single molecule chelating the iron in a bidentate manner. The binding mode of a hydroxamic acid analogue, at least in the crystalline state, is unusual because two molecules of the inhibitor are observed at the active site and partial displacement of the iron binding aspartyl residue was observed. [Copyright &y& Elsevier]

Abstract: Thirty-six novel acylurea connected straight chain hydroxamates were designed and synthesized. Structure–activity relationships (SAR) were established for the length of linear chain linker and substitutions on the benzoylurea group. Compounds 5g, 5i, 5n, and 19 showed 10–20-fold enhanced HDAC1 potency compared to SAHA. In general, the cellular potency pIC50 (COLO205) correlates with enzymatic potency pIC50 (HDAC1). Compound 5b (SB207), a structurally simple and close analogue to SAHA, is more potent against HDAC1 and HDAC6 compared to the latter. As a representative example of this series, good in vitro enzymatic and cellular potency plus an excellent pharmacokinetic profile has translated into better efficacy than SAHA in both prostate cancer (PC3) and colon cancer (HCT116) xenograft models. [Copyright &y& Elsevier]

Abstract: Ongoing effort to gather further knowledge about the structural requirements on histone deacetylase inhibitors led to the synthesis of novel N-hydroxybenzamide-based HDAC inhibitors 1a–o, introducing branched hydrophobic groups at the capping group, and their inhibition activity against HDACs and anti-proliferation activity in four tumor cell lines were determined. Compounds 1j–o were further tested against recombinant human HDAC1 and HDAC4 to evaluate their selectivity profile. This work further suggests that the chemical nature of the capping group is critical for subtle discrimination between the class I and the class II HDAC isoforms. [Copyright &y& Elsevier]

Abstract: A serendipitous discovery that the metalloprotease binding profile of a novel class of 2-carboxamide-3-hydroxamic acid piperidines could be significantly attenuated by the modification of the unexplored P1 substituent enabled the design and synthesis of a novel 2-carboxamide-1-hydroxamic acid cyclohexyl scaffold core that exhibited excellent HER-2 potency and unprecedented MMP-selectivity that we believe would not have been possible via conventional P1′ perturbations. [Copyright &y& Elsevier]

Abstract: A series of N-hydroxy-1,2-disubstituted-1H-benzimidazol-5-yl acrylamides were designed and synthesized as novel HDAC inhibitors. General SAR has been established for the substituents at positions 1 and 2, as well as the importance of the ethylene group and its attachment to position 5. Optimized compounds are much more potent than SAHA in both enzymatic and cellular assays. A representative compound, 23 (SB639), has demonstrated antitumor activity in a colon cancer xenograft model. [Copyright &y& Elsevier]

Abstract: In an effort to obtain a MMP selective and potent inhibitor of HER-2 sheddase (ADAM-10), the P1′ group of a novel class of (6S,7S)-7-[(hydroxyamino)carbonyl]-6-carboxamide-5-azaspiro[2.5]octane-5-carboxylates was attenuated and the structure–activity relationships (SAR) will be discussed. In addition, it was discovered that unconventional perturbation of the P2′ moiety could confer MMP selectivity, which was hypothesized to be a manifestation of the P2′ group effecting global conformational changes. [Copyright &y& Elsevier]

Abstract: A series of ω-alkoxy ethers were prepared with variation of the length of the aliphatic chain of suberoylanilide hydroxamic acid (SAHA, vorinostat). Eight carbon long chain analogues showed the best activity, among which several substituted benzyl ether derivatives exhibited inhibitory activity on HDAC comparable to SAHA, and antiproliferative activity on three human cell lines (NB4, H460, and HCT-116) better than SAHA. However, no significant difference in antiproliferative activity was observed between two enantiomers bearing the benzyl ether moiety. [Copyright &y& Elsevier]

Abstract: We designed and synthesized hydroxamic acid derivatives bearing a 4-(3-pyridyl)phenyl group as a cap structure, and found that they exhibit potent histone deacetylase (HDAC) inhibitory activity. A representative compound, 17a, showed more potent growth-inhibitory activity against pancreatic cancer cells and greater upregulation of p21WAF1/CIP1 expression than the clinically used HDAC inhibitor suberoylanilide hydroxamic acid (Zolinza™). [Copyright &y& Elsevier]

Abstract: Here we describe the inhibitory activity toward neutral aminopeptidase of three new families of phosphinate inhibitors related in structure to hydroxamic acids. These compounds, even as racemic mixtures, are good inhibitors of APN and show strong structure activity relationship (SAR) depending on the substituents in P1 and P1′ positions. [Copyright &y& Elsevier]

Abstract: The design, synthesis, and enzyme kinetics evaluation of a transition-state inhibitor of glyoxalase-I is described. The union of the hydroxamic acid zinc-chelator with a urea isostere for the glu–cys amide bond led to a glutathione analog which retained inhibitory potency toward glyoxalase-I while possessing resistance toward γ-glutamyltranspeptidase mediated breakdown. This compound is viewed as a potential lead for the development of second-generation glyoxalase-I inhibitors wherein, the problems pertaining to metabolism and selectivity are overcome. [Copyright &y& Elsevier]

Abstract: A novel series of achiral TNF-α converting enzyme (TACE) inhibitors has been discovered. These compounds exhibited activities from 0.35 to 11nM in a porcine TACE assay and inhibited TNF-α production in an LPS-stimulated whole blood assay with an IC50 value of 23nM for the most potent one. They also have excellent selectivities over related metalloproteases including aggrecanases. [Copyright &y& Elsevier]

Recent studies have highlighted a key role in regulating gene transcription, in both eukaryotes and prokaryotes, by enzymes that control the acetylation and deacetylation of histones. In particular, inhibitors of histone deacetylases (HDAC-Is) have been shown effective in controlling the development of many parasites, such as the plasmodium of malaria. Here we report the results of a study aimed at evaluating antiparasitic effect of two classes of HDAC-Is bearing different zinc binding group (hydroxamic acid vs thiol). The study showed that only the hydroxamic acid based HDAC inhibitors were active, with Plasmodium falciparum being the most sensitive parasite, having from low double-digit to single-digit nanomolar range in vitro activities. Among three derivatives evaluated also in vivo, ST8086AA1 ( 8 ) effectively inhibited 88% of the development of Plasmodium falciparum . [ABSTRACT FROM AUTHOR]