Natural products have long been recognized as a rich source of potent therapeutics but further development is often limited by high structural complexity and high molecular weight. In contrast, at the core of the thujaplicins is a lead-like tropolone scaffold characterized by relatively low molecular weight, ample sites for diversification, and metal-binding functionality poised for targeting a range of metalloenzyme drug targets. Here, we describe the development of this underutilized scaffold for the discovery of tropolone derivatives that function as isozyme-selective inhibitors of the validated anticancer drug target, histone deacetylase (HDAC). Several monosubstituted tropolones display remarkable levels of selectivity for HDAC2 and potently inhibit the growth of T-cell lymphocyte cell lines. The tropolones represent a new chemotype of isozyme-selective HDAC inhibitors. KEYWORDS: Tropolone, HDAC, isozyme-selectivity, thujaplicin, metalloenzyme, T-lymphocyte cancer cell lines N atural products have long served as a rich source of drugs for a variety of indications ranging from anticancer to antimicrobial to neurological disorders. Typically these natural products are characterized by high molecular weight and potency as well as high levels of structural complexity with limited sites for diversification. In contrast, thujaplicins, members of the tropolone family of natural products, can be regarded as lead-like natural products. β-Thujaplicin (also known as hinokitiol) is characterized by low molecular weight (MW = 164) and a relatively lower level of complexity that allows more extensive structural modification. Thujaplicins are monoterpene natural products isolated from the heartwood of trees in the Cupressaceae family 1 that are associated with antiproliferative activity.2−4 There have been few attempts to utilize these lead-like compounds in drug discovery, perhaps exacerbated by limited synthetic accessibility to these nonbenzenoid aromatics.The tropolone functionality is uniquely disposed to strongly chelate metal ions, which may be a hallmark of the biological activity of these compounds.3 Substituted tropolones are a compelling and distinct chemotype for the development of inhibitors of metalloenzyme drug targets. Herein, we describe our efforts to use β-thujaplicin as a lead-like natural product to develop a novel class of inhibitors of histone deacetylase, a validated target in the treatment of cancer. 5,6 Of the 18 HDAC isoforms, 11 are metalloenzymes that use zinc to remove a terminal acetyl group from lysine residues present in histones and other client proteins. The reversible acetylation and hydrolysis of the ε-acetamide in histones is associated with regulation of gene expression. Interestingly, there are a variety of natural products that inhibit HDACs such as trichostatin A (TSA; Figure 1), romidepsin, and trapoxin. Both romidepsin and vorinostat were approved by the FDA for the treatment of cutaneous T-cell lymphoma; the latter possesses a zinc-targeting hydroxamate, similar to TS...

A dark-brown tuft-forming cyanobacterium, morphologically resembling the genus Symploca, was collected during an expedition to the Coiba National Park, a UNESCO World Heritage Site on the Pacific coast of Panama. Phylogenetic analysis of its 16S rRNA gene sequence indicated that it is 4.5% divergent from the type strain for Symploca, and thus is likely a new genus. Fractionation of the crude extract led to the isolation of a new cytotoxin, designated santacruzamate A (1), which has several structural features in common with suberoylanilide hydroxamic acid [(2), SAHA, trade name Vorinostat®], a clinically approved histone deacetylase (HDAC) inhibitor used to treat refractory cutaneous T-cell lymphoma. Recognition of the structural similarly of 1 and SAHA led to the characterization of santacruzamate A as a picomolar level selective inhibitor of HDAC2, a Class I HDAC, with relatively little inhibition of HDAC4 or HDAC6, both Class II HDACs. As a result, chemical syntheses of santacruzamate A as well as a structurally intriguing hybrid molecule, which blends aspects of both agents (1 and 2), were achieved and evaluated for their HDAC activity and specificity.

BackgroundMolecular heterogeneity of tumors suggests the presence of multiple different subclones that may limit response to targeted therapies and contribute to acquisition of drug resistance, but its quantification has remained challenging.ResultsWe performed simulations to evaluate statistical measures that best capture the molecular diversity within a group of tumors for either continuous (gene expression) or discrete (mutations, copy number alterations) molecular data. Dispersion based metrics in the principal component space best captured the underlying heterogeneity. To demonstrate utility of these measures, we characterized the diversity in transcriptional and genomic profiles of different breast tumor subtypes, and showed that basal-like or triple-negative breast cancers (TNBC) are significantly more heterogeneous molecularly than other subtypes. Our analysis also suggests that transcriptional diversity is a global characteristic of the tumors observed across the majority of molecular pathways. Among basal-like tumors, those that were resistant to multi-agent chemotherapy showed greater transcriptional diversity compared to chemotherapy-sensitive tumors, suggesting that potentially multiple mechanisms may be contributing to chemotherapy resistance.ConclusionsWe proposed and validated measures of transcriptional and genomic diversity that can quantify the molecular diversity of tumors. We applied the new measures to genomic data from breast tumors and demonstrated that basal-like breast cancers are significantly more diverse than other breast cancers. The observation that chemo-resistant tumors are significantly more diverse molecularly than chemosensitive tumors implies that multiple resistance mechanisms may be active, thus limiting the sensitivity and accuracy of predictive markers of chemotherapy response.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-876) contains supplementary material, which is available to authorized users.

Background Tissue handling can alter global gene expression potentially affecting the analytical performance of genomic signatures, but such effects have not been systematically evaluated. Methods Tissue samples from 11 previously untreated breast tumors were minced and aliquots were either snap frozen or placed in RNAlater immediately or after 20, 40, 60, 120 or 180 minutes at room temperature. RNA was profiled on Affymetrix HG-U133A arrays. We used probe-set-wise hierarchical models to evaluate the effect of preservation method on transcript expression and linear mixed effects models to assess the effect of cold ischemic delay on the expression of individual probe sets. Gene set enrichment analysis identified pathways overrepresented in the affected transcripts. We combined the levels of 41 most sensitive transcripts to develop an index of ischemic stress. Results Concordance in global gene expression between the baseline and 40 min delay was higher for samples preserved in RNAlater (average concordance correlation coefficient CCC = 0.92 compared to 0.88 for snap frozen). Overall, 481 transcripts (3%) were significantly affected by the preservation method, most of them involved in processes important in cancer. Prolonged cold ischemic delay of up to 3 hours induced marginal global gene expression changes (average CCC=0.90 between baseline and 3 hour delay). However 41 transcripts were significantly affected by cold ischemic delay. Among the induced transcripts were stress response genes, apoptotic response genes; among the downregulated were genes involved in metabolism, protein processing and cell cycle regulation. An index combining the expression levels of these genes was proportional to the cold ischemic delay. Conclusions Prolonged cold ischemia induces significant transcriptional changes in a small subset of transcripts in the tissue. Furthermore, the expression level of about 3% of the transcripts is affected by the preservation method. These sensitive transcripts should not be included in genomic signatures for more reliable analytical performance.

Since post-translational modifications of proteins are key mechanisms for controlling cellular function, targeting the machinery involved in these modifications offers new opportunities for the development of therapeutic agents. The histone deacetylases (HDACs) represent an important family of enzymes that are involved in controlling the acetylation state of key lysine residues in histones and other proteins. The development of HDAC inhibitors for the treatment of several diseases, most notably cancer, has proceeded rapidly. Recent attention has turned towards the development of isozyme-specific inhibitors that will provide selective targeting. It is believed that the ability to target-specific HDACs rather than all family members will lead to superior therapeutics with better efficacy and lower toxicity. A review of recent patents shows that researchers are targeting a wide range of isozymes and that key advances in the structural biology of HDACs are providing important design information.