Verbascoside Elicits Its Beneficial Effects by Enhancing Mitochondrial Spare Respiratory Capacity and the Nrf2/HO-1 Mediated Antioxidant System in a Murine Skeletal Muscle Cell Line.

Muscle weakness and muscle loss characterize many physio-pathological conditions, including sarcopenia and many forms of muscular dystrophy, which are often also associated with mitochondrial dysfunction. Verbascoside, a phenylethanoid glycoside of plant origin, also named acteoside, has shown strong antioxidant and anti-fatigue activity in different animal models, but the molecular mechanisms underlying these effects are not completely understood. This study aimed to investigate the influence of verbascoside on mitochondrial function and its protective role against H2O2-induced oxidative damage in murine C2C12 myoblasts and myotubes pre-treated with verbascoside for 24 h and exposed to H2O2. We examined the effects of verbascoside on cell viability, intracellular reactive oxygen species (ROS) production and mitochondrial function through high-resolution respirometry. Moreover, we verified whether verbascoside was able to stimulate nuclear factor erythroid 2-related factor (Nrf2) activity through Western blotting and confocal fluorescence microscopy, and to modulate the transcription of its target genes, such as heme oxygenase-1 (HO-1) and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), by Real Time PCR. We found that verbascoside (1) improved mitochondrial function by increasing mitochondrial spare respiratory capacity; (2) mitigated the decrease in cell viability induced by H2O2 and reduced ROS levels; (3) promoted the phosphorylation of Nrf2 and its nuclear translocation; (4) increased the transcription levels of HO-1 and, in myoblasts but not in myotubes, those of PGC-1α. These findings contribute to explaining verbascoside's ability to relieve muscular fatigue and could have positive repercussions for the development of therapies aimed at counteracting muscle weakness and mitochondrial dysfunction.

Remarks on Mitochondrial Myopathies.

Mitochondrial myopathies represent a heterogeneous group of diseases caused mainly by genetic mutations to proteins that are related to mitochondrial oxidative metabolism. Meanwhile, a similar etiopathogenetic mechanism (i.e., a deranged oxidative phosphorylation and a dramatic reduction of ATP synthesis) reveals that the evolution of these myopathies show significant differences. However, some physiological and pathophysiological aspects of mitochondria often reveal other potential molecular mechanisms that could have a significant pathogenetic role in the clinical evolution of these disorders, such as: i. a deranged ROS production both in term of signaling and in terms of damaging molecules; ii. the severe modifications of nicotinamide adenine dinucleotide (NAD)+/NADH, pyruvate/lactate, and α-ketoglutarate (α-KG)/2- hydroxyglutarate (2-HG) ratios. A better definition of the molecular mechanisms at the basis of their pathogenesis could improve not only the clinical approach in terms of diagnosis, prognosis, and therapy of these myopathies but also deepen the knowledge of mitochondrial medicine in general.

Mitochondrial Metabolism in Cancer. A Tangled Topic. Which Role for Proteomics?

Given the role of mitochondria in modulating many cellular functions, it is not surprising that they can play a crucial role also in molecular pathophysiology of cancer. In particular, the discovery in recent decades of a link between cancer metabolic processes, alterations of mitochondrial DNA, oncogenes and tumor suppressors has led not only to a renaissance of interest in Warburg's pioneering work, but also to a reexamination of his original observations above all in relation to the current knowledge in cancer cell metabolism. It follows that, although mitochondrial contribution to the pathogenesis of cancer has historically tended to be neglected, it is now evident that reprogrammed mitochondria can contribute to a complex bioenergetic adjustment that sustains not only tumor formation but also its progression. Most importantly, cancer cell metabolism seems to have a role in diversified aspects related to cancer pathophysiology (i.e., aggressiveness, recurrence, metastatic dissemination). Hence, it is imperative to always consider cancer cell metabolism, its adaptability, its influences but, above all, its functional heterogeneity in a single tumor, for a really rational and valid approach towards molecular biology of cancer.

Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative.

The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed data sets were analyzed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and submitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted in nodes of this network but with a different ability in coisolating mitochondria-associated structures for each enrichment protocol/cell line pair.

The epithelial-mesenchymal transition in cancer: a potential critical topic for translational proteomic research.

The epithelial-mesenchymal transition (EMT) is a morphogenetic process that results in a loss of epithelial characteristics and the acquisition of a mesenchymal phenotype. First described in embryogenesis, the EMT has been recently implicated in carcinogenesis and tumor progression. In addition, recent evidence has shown that stem-like cancer cells present the hallmarks of the EMT. Some of the molecular mechanisms related to the interrelationships between cancer pathophysiology and the EMT are well-defined. Nevertheless, the precise molecular mechanism by which epithelial cancer cells acquire the mesenchymal phenotype remains largely unknown. This review focuses on various proteomic strategies with the goal of better understanding the physiological and pathological mechanisms of the EMT process.

The Role of CA 125 as Tumor Marker: Biochemical and Clinical Aspects.

CA 125 also known as mucin 16 or MUC16 is a large membrane glycoprotein belonging to the wide mucin family, encoded by the homonymous MUC16 gene. Following its discovery in the blood of some patients with specific types of cancers or other benign conditions, CA125 has found application as a tumor marker of ovarian cancer. Thirty years after its discovery, use of CA 125 is still FDA-recommended to monitor response to therapy in patients with epithelial ovarian cancer and to detect residual or recurrent disease in patients who have undergone first-line therapy and would be considered for second-look procedures. However, due to its limited specificity and sensitivity, CA 125 alone cannot still be an ideal biomarker. Increased clinical performance, in terms of better sensitivity and specificity in identifying epithelial ovarian cancer relapse, has been obtained by combined use of CA 125 with HE4, another ovarian cancer marker recently introduced in clinical use. Significant advancements have been achieved more recently, due to the introduction of FDA-approved ROMA and OVA1 algorithms to evaluate the risk of ovarian cancer for patients with a pelvic mass.

CA 19-9: Biochemical and Clinical Aspects.

CA19-9 (carbohydrate antigen 19-9, also called cancer antigen 19-9 or sialylated Lewis a antigen) is the most commonly used and best validated serum tumor marker for pancreatic cancer diagnosis in symptomatic patients and for monitoring therapy in patients with pancreatic adenocarcinoma. Normally synthesized by normal human pancreatic and biliary ductal cells and by gastric, colon, endometrial and salivary epithelia, CA 19-9 is present in small amounts in serum, and can be over expressed in several benign gastrointestinal disorders. Importantly, it exhibits a dramatic increase in its plasmatic levels during neoplastic disease. However, several critical aspects for its clinical use, such as false negative results in subjects with Lewis (a-b-) genotype and false positive elevation, occasional and transient, in patients with benign diseases, together with its poor positive predictive value (72.3 %), do not make it a good cancer-specific marker and renders it impotent as a screening tool. In the last years a large number of putative biomarkers for pancreatic cancer have been proposed, most of which is lacking of large scale validation. In addition, none of these has showed to possess the requisite sensitivity/specificity to be introduced in clinical use. Therefore, although with important limitations we well-know, CA 19-9 continues being the only pancreatic cancer marker actually in clinical use.

Neuron-Specific Enolase as a Biomarker: Biochemical and Clinical Aspects.

Neuron-specific enolase (NSE) is known to be a cell specific isoenzyme of the glycolytic enzyme enolase. In vertebrate organisms three isozymes of enolase, expressed by different genes, are present: enolase α is ubiquitous; enolase ß is muscle-specific and enolase γ is neuron-specific. The expression of NSE, which occurs as γγ- and αγ-dimer, is a late event in neural differentiation, thus making it a useful index of neural maturation.NSE is a highly specific marker for neurons and peripheral neuroendocrine cells. As a result of the findings of NSE in specific tissues under normal conditions, increased body fluids levels of NSE may occur with malignant proliferation and thus can be of value in diagnosis, staging and treatment of related neuroendocrine tumours (NETs).NSE is currently the most reliable tumour marker in diagnosis, prognosis and follow-up of small cell lung cancer (SCLC), even though increased levels of NSE have been reported also in non-small cell lung cancer (NSCLC). The level of NSE correlates with tumour burden, number of metastatic sites and response to treatment.NSE can be also useful at diagnosis of NETs and gastroenteropancreatic (GEP)-NETs.Raised serum levels of NSE have been found in all stages of neuroblastoma, although the incidence of increased concentration is greater in widespread and metastatic disease. Moreover, NSE determination in cord blood offers an early postnatal possibility of confirming the diagnosis of neuroblastoma in newborns.NSE has been demonstrated to provide quantitative measures of brain damage and/or to improve the diagnosis and the outcome evaluation in ischaemic stroke, intracerebral hemorrhage, seizures, comatose patients after cardiopulmonary resuscitation for cardiac arrest and traumatic brain injury.Increased NSE serum levels have also been found associated with melanoma, seminoma, renal cell carcinoma, Merkel cell tumour, carcinoid tumours, dysgerminomas and immature teratomas, malignant phaechromocytoma, Guillain-Barré syndrome and Creutzfeldt-Jakob disease.

A Critical Approach to Clinical Biochemistry of Chromogranin A.

Chromogranin A (CGA) is a member of the granin family of proteins which are widespread in endocrine, neuroendocrine, peripheral, and central nervous tissues, where they are typically found in secretory granules. It is well accepted that CGA cooperates to regulate synthesis and secretion of these various granule signaling molecules.Because of its ubiquitous distribution within neuroendocrine tissues, CGA can be a useful diagnostic marker for neuroendocrine neoplasms, including carcinoids, pheochromocytomas, neuroblastomas, medullary thyroid carcinomas (MTC), some pituitary tumors, functioning and nonfunctioning islet cell tumors and other amine precursor uptake and decarboxylation (APUD) tumors. It is also useful as a prognostic marker for detection of recurrence and monitoring of response to different treatments. As other tumor markers, it is imperative to know its physiology and pathophysiology, its sensitivity and specificity in different neuroendocrine tumors (NETs), and carefully integrate these data with the clinical data of the single patient, to maximize its diagnostic/prognostic index.

Circulating tumour cells and cancer stem cells: a role for proteomics in defining the interrelationships between function, phenotype and differentiation with potential clinical applications.

Research on the discovery and implementation of valid cancer biomarkers is one of the most challenging fields in oncology and oncoproteomics in particular. Moreover, it is generally accepted that an evaluation of cancer biomarkers from the blood could significantly enable biomarker assessments by providing a relatively non-invasive source of representative tumour material. In this regard, circulating tumour cells (CTCs) isolated from the blood of metastatic cancer patients have significant promise. It has been demonstrated that localised and metastatic cancers may give rise to CTCs, which are detectable in the bloodstream. Despite technical difficulties, recent studies have highlighted the prognostic significance of the presence and number of CTCs in the blood. Future studies are necessary not only to detect CTCs but also to characterise them. Furthermore, another pathogenically significant type of cancer cells, known as cancer stem cells (CSCs) or more recently termed circulating tumour stem cells (CTSCs), appears to have a significant role as a subpopulation of CTCs. This review discusses the potential application of proteomic methodologies to improve the isolation and characterisation of CTCs and to distinguish between CTCs with a poor clinical significance and those with important biological and clinical implications.

The polyphenolic compound punicalagin protects skin fibroblasts from UVA radiation oxidative damage.

Polyphenols are a class of natural compounds that act as antioxidants, neutralising harmful free radicals that would damage cells and increase the risk of diseases such as cancer, diabetes and heart disease. They also reduce inflammation, which is thought to be at the root of many chronic diseases. We are investigating the photoprotective effects of punicalagin, a type of polyphenolic compound mainly found in pomegranates, against UVA-induced damage in human skin fibroblasts. Punicalagin increases cell viability and reduces the high levels of ROS generated by photooxidative stress through its ability to modulate the Nrf2 transcriptional pathway. Interestingly, activation of the Nrf2 pathway results in an increase in reduced glutathione, NADH, and subsequently protects mitochondrial respiratory capacity. Integrating molecular and imaging approaches, our results demonstrate a potential cytoprotective effect of punicalagin against UVA-induced skin damage through an anti-apoptotic mechanism.

Rutin Protects Fibroblasts from UVA Radiation through Stimulation of Nrf2 Pathway.

This study explores the photoprotective effects of rutin, a bioflavonoid found in some vegetables and fruits, against UVA-induced damage in human skin fibroblasts. Our results show that rutin increases cell viability and reduces the high levels of ROS generated by photo-oxidative stress (1 and 2 h of UVA exposure). These effects are related to rutin's ability to modulate the Nrf2 transcriptional pathway. Interestingly, activation of the Nrf2 signaling pathway results in an increase in reduced glutathione and Bcl2/Bax ratio, and the subsequent protection of mitochondrial respiratory capacity. These results demonstrate how rutin may play a potentially cytoprotective role against UVA-induced skin damage through a purely antiapoptotic mechanism.

Mitochondrial proteomic approaches for new potential diagnostic and prognostic biomarkers in cancer.

Mitochondrial dysfunction and mutations in mitochondrial DNA have been implicated in a wide variety of human diseases, including cancer. In recent years, considerable advances in genomic, proteomic and bioinformatic technologies have made it possible the analysis of mitochondrial proteome, leading to the identification of over 1,000 proteins which have been assigned unambiguously to mitochondria. Defining the mitochondrial proteome is a fundamental step for fully understanding the organelle functions as well as mechanisms underlying mitochondrial pathology. In fact, besides giving information on mitochondrial physiology, by characterizing all the components of this subcellular organelle, the application of proteomic technologies permitted now to study the proteins involved in many crucial properties in cell signaling, cell differentiation and cell death and, in particular, to identify mitochondrial proteins that are aberrantly expressed in cancer cells. An improved understanding of the mitochondrial proteome could be essential to shed light on the connection between mitochondrial dysfunction, deregulation of apoptosis and tumorigenesis and to discovery new therapeutic targets for mitochondria-related diseases.

Mitochondrial Respiratory Complexes as Targets of Drugs: The PPAR Agonist Example.

Mitochondrial bioenergetics are progressively acquiring significant pathophysiological roles. Specifically, mitochondria in general and Electron Respiratory Chain in particular are gaining importance as unintentional targets of different drugs. The so-called PPAR ligands are a class of drugs which not only link and activate Peroxisome Proliferator-Activated Receptors but also show a myriad of extrareceptorial activities as well. In particular, they were shown to inhibit NADH coenzyme Q reductase. However, the molecular picture of this intriguing bioenergetic derangement has not yet been well defined. Using high resolution respirometry, both in permeabilized and intact HepG2 cells, and a proteomic approach, the mitochondrial bioenergetic damage induced by various PPAR ligands was evaluated. Results show a derangement of mitochondrial oxidative metabolism more complex than one related to a simple perturbation of complex I. In fact, a partial inhibition of mitochondrial NADH oxidation seems to be associated not only with hampered ATP synthesis but also with a significant reduction in respiratory control ratio, spare respiratory capacity, coupling efficiency and, last but not least, serious oxidative stress and structural damage to mitochondria.

A proteomic approach to characterizing ciglitazone-induced cancer cell differentiation in Hep-G2 cell line.

Drug induced cell differentiation represents a promising experimental model for proteomic analysis of cancer cells. In fact, by modulating and monitoring neoplastic cell differentiation it could be possible to identify cytodifferentiation related protein expression changes that can be subsequently utilized in vivo as potential cancer biomarkers. One main advantage of this approach is the significant reduction of biological variability normally observed in clinical biomarker research, with important implications also in prognosis and therapy. At this regard, a new class of differentiating agents is emerging, the so called PPAR-ligands, which however are characterized by a debated mechanism of action that has not been yet studied through a proteomic approach. To this aim, we investigated ciglitazone-induced differentiation of a human hepatocarcinoma HepG2 cell line, by monitoring biochemical and cellular parameters of cytodifferentiation and modifications of cellular protein profiles through 2-DE and MALDI-TOF analysis. Independent of the hypothesized mechanism of action of this intriguing PPARgamma agonist, results indicated that ciglitazone is a strong differentiating agent for the HepG2 cell line and that this process is associated with modifications of protein expression related to cell antioxidant systems, the cell cycle apparatus, signal transduction pathways, cellular stress and invasiveness. At last, considering these and other published data, a proteomic profile related to the cancer aggressiveness is beginning to emerge.

The Tangled Mitochondrial Metabolism in Cancer: An Innovative Pharmacological Approach.

BACKGROUND: Mitochondria are remarkably gaining significant and different pathogenic roles in cancer (i.e., to sustain specific metabolism, to activate signaling pathways, to promote apoptosis resistance, to favor cancer cell dissemination, and finally to facilitate genome instability). Interestingly, all these roles seem to be linked to the fundamental activity of mitochondria, i.e. oxidative metabolism. Intriguingly, a typical modification of mitochondrial oxidative metabolism and reactive oxygen species production/ neutralization seems to have a central role in all these tangled pathogenic roles in cancer. On these bases, a careful understanding of the molecular relationships between cancer and mitochondria may represent a fundamental step to realize therapeutic approaches blocking the typical cancer progression. The main aim of this review is to stress some neglected aspects of oxidative mitochondrial metabolism of cancer cells to promote more translational research with diagnostic and therapeutic potential. METHODS: We reviewed the available literature regarding clinical and experimental studies on various roles of mitochondria in cancer, with attention to the cancer cell mitochondrial metabolism. RESULTS: Mitochondria are an important source of reactive oxygen species. Their toxic effects seem to increase in cancer cells. However, it is not clear if damage depends on ROS overproduction and/or defect in detoxification. Failure of both these processes is likely a critical component of the cancer process and is strictly related to the actual microenvironment of cancer cells. CONCLUSIONS: Mitochondria, also by ROS production, have a fundamental pathogenetic role in promoting and maintaining cancer and its spreading. To carefully understand the tangled redox state of cancer cells mitochondria represents a fundamental step to realize therapeutic approaches blocking the typical cancer progression.

Mitochondria, ciglitazone and liver: a neglected interaction in biochemical pharmacology.

Peroxisome proliferator activated receptors (PPARs) are a class of nuclear receptors now actively investigated for their involvement in lipid and glucidic metabolism, immune regulation and cell differentiation. Drugs binding and activating PPARs are therefore attracting attention for their potential therapeutic role in various diseases like type 2 diabetes, dyslipidemias, atherosclerosis, obesity (i.e., metabolic syndrome). Agonists of these receptors have been already used in therapeutic protocols: fibrates (PPAR-alpha ligands) are being used in hyperlipidemias, and thiazolidinediones (mainly PPAR-gamma ligands) are being employed as insulin sensitizers. The latter drugs introduction into therapy, however, showed very soon some unwanted effects (hepatotoxicity at first and myocardiotoxicity later on) which confirmed some contradictory data already suggested by pre-clinical trial-experiments. In this study we show that some PPAR ligands impair mitochondrial oxidative metabolism in human liver cell line mainly by deranging NADH oxidation. Intriguingly, the PPAR-gamma ligand ciglitazone caused a dose-dependent inhibition of NADH-cytochrome c reductase that resulted, at a drug concentration of 50 microM, of about 60% (P<0.001), while other PPAR ligands with different receptor affinity - positive controls like clofibrate (0.7 mM), gemfibrozil (0.23 mM) and bezafibrate (1 mM) - reduced the activity of mitochondrial Complex I by about 20% (P<0.01, P<0.01 and P<0.05, respectively). The induced mitochondrial dysfunction imposed a series of metabolic compensatory adaptations characterized by a significant shift to anaerobic glycolysis. These findings underline the undervalued non-genomic effects of PPAR ligands and can provide a better understanding of the pharmacotoxicological profiles of these drugs and of their roles in the therapy of diabetes mellitus.

Cryoglobulin Test and Cryoglobulinemia Hepatitis C-Virus Related.

Cryoglobulins are immunoglobulins that precipitate in serum at temperatures below 37°C and resolubilize upon warming. The clinical syndrome of cryoglobulinemia usually includes purpura, weakness, and arthralgia, but the underlying disease may also contribute other symptoms. Blood samples for cryoglobulin are collected, transported, clotted and spun at 37°C, before the precipitate is allowed to form when serum is stored at 4°C in a Wintrobe tube for at least seven days. The most critical and confounding factor affecting the cryoglobulin test is when the preanalytical phase is not fully completed at 37°C. The easiest way to quantify cryoglobulins is the cryocrit estimate. However, this approach has low accuracy and sensitivity. Furthermore, the precipitate should be resolubilized by warming to confirm that it is truly formed of cryoglobulins. The characterization of cryoglobulins requires the precipitate is several times washed, before performing immunofixation, a technique by which cryoglobulins can be classified depending on the characteristics of the detected immunoglobulins. These features imply a pathogenic role of these molecules which are consequently associated with a wide range of symptoms and manifestations. According to the Brouet classification, Cryoglobulins are grouped into three types by the immunochemical properties of immunoglobulins in the cryoprecipitate. The aim of this paper is to review the major aspects of cryoglobulinemia and the laboratory techniques used to detect and characterize cryoglobulins, taking into consideration the presence and consequences of cryoglobulinemia in Hepatitis C Virus (HCV) infection.

3-(4-Aroyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamides as a new class of synthetic histone deacetylase inhibitors. 2. Effect of pyrrole-C2 and/or -C4 substitutions on biological activity.

Previous SAR studies (Part 1: Mai, A.; et al. J. Med. Chem. 2003, 46, 512-524) performed on some portions (pyrrole-C4, pyrrole-N1, and hydroxamate group) of 3-(4-benzoyl-1-methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamide (1a) highlighted its 4-phenylacetyl (1b) and 4-cynnamoyl (1c) analogues as more potent compounds in inhibiting maize HD2 activity in vitro. In the present paper, we investigated the effect on anti-HD2 activity of chemical substitutions performed on the pyrrole-C2 ethene chains of 1a-c, which were replaced with methylene, ethylene, substituted ethene, and 1,3-butadiene chains (compounds 2). Biological results clearly indicated the unsubstituted ethene chain as the best structural motif to get the highest HDAC inhibitory activity, the sole exception to this rule being the introduction of the 1,3-butadienyl moiety into the 1a chemical structure (IC50(2f) = 0.77 microM; IC50(1a) = 3.8 microM). IC50 values of compounds 3, prepared as 1b homologues, revealed that between benzene and carbonyl groups at the pyrrole-C(4) position a hydrocarbon spacer length ranging from two to five methylenes is well accepted by the APHA template, being that 3a (two methylenes) and 3d (five methylenes) are more potent (2.3- and 1.4-fold, respectively) than 1b, while the introduction of a higher number of methylene units (see 3e,f) decreased the inhibitory activities of the derivatives. Particularly, 3a (IC50 = 0.043 microM) showed the same potency as SAHA in inhibiting HD2 in vitro, and it was 3000- and 2.6-fold more potent than sodium valproate and HC-toxin and was 4.3- and 6-fold less potent than trapoxin and TSA, respectively. Finally, conformationally constrained forms of 1b,c (compounds 4), prepared with the aim to obtain some information potentially useful for a future 3D-QSAR study, showed the same (4a,b) or higher (4c,d) HD2 inhibiting activities in comparison with those of the reference drugs. Molecular modeling and docking calculations on the designed compounds performed in parallel with the chemistry work fully supported the synthetic effort and gave insights into the binding mode of the more flexible APHA derivatives (i.e., 3a). Despite the difference of potency between 1b and 3a in the enzyme assay, the two APHA derivatives showed similar antiproliferative and cytodifferentiating activities in vivo on Friends MEL cells, being that 3a is more potent than 1b in the differentiation assay only at the highest tested dose (48 microM).

3-(4-Aroyl-1-methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamides as a new class of synthetic histone deacetylase inhibitors. 3. Discovery of novel lead compounds through structure-based drug design and docking studies.

Aroyl-pyrrole-hydroxy-amides (APHAs) are a new class of synthetic HDAC inhibitors recently described by us. Through three different docking procedures we designed, synthesized, and tested two new isomers of APHA lead compound 3-(4-benzoyl-1-methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamide (1), compounds 3 and 4, characterized by different insertions of benzoyl and propenoylhydroxamate groups onto the pyrrole ring. Biological activities of 3 and 4 were predicted by computational tools up to 617-fold more potent than that of 1 against HDAC1; thus, 3 and 4 were synthesized and tested against both mouse HDAC1 and maize HD2 enzymes. Predictions of biological affinities (K(i) values) of 3 and 4, performed by a VALIDATE model (applied on either SAD or automatic DOCK or Autodock results) and by the Autodock internal scoring function, were in good agreement with experimental activities. Ligand/receptor positive interactions made by 3 and 4 into the catalytic pocket, in addition to those showed by 1, could at least in part account for their higher HDAC1 inhibitory activities. In particular, in mouse HDAC1 inhibitory assay 3 and 4 were 19- and 6-times more potent than 1, respectively, and 3 and 4 antimaize HD2 activities were 16- and 76-times higher than that of 1, 4 being as potent as SAHA in this assay. Compound 4, tested as antiproliferative and cytodifferentiating agent on MEL cells, showed dose-dependent growth inhibition and hemoglobin accumulation effects.