Histone deacetylase inhibitors suppress thymidylate synthase gene expression and synergize with the fluoropyrimidines in colon cancer cells

Despite recent therapeutic advances, the response rates to chemotherapy for patients with metastatic colon cancer remain at approximately 50% with the fluoropyrimidine, 5-fluorouracil (5-FU), continuing to serve as the foundation chemotherapeutic agent for the treatment of this disease. Previous studies have demonstrated that overexpression of thymidylate synthase (TS) is a key determinant of resistance to 5-FU-based chemotherapy. Therefore, there is a significant need to develop alternative therapeutic strategies to overcome TS-mediated resistance. In this study, we demonstrate that the histone deacetylase inhibitors (HDACi) vorinostat and LBH589 significantly downregulate TS gene expression in a panel of colon cancer cell lines. Downregulation of TS was independent of p53, p21 and HDAC2 expression and was achievable in vivo as demonstrated by mouse xenograft models. We provide evidence that HDACi treatment leads to a potent transcriptional repression of the TS gene. Combination of the fluoropyrimidines 5-FU or FUdR with both vorinostat and LBH589 enhanced cell cycle arrest and growth inhibition. Importantly, the downstream effects of TS inhibition were significantly enhanced by this combination including the inhibition of acute TS induction and the enhanced accumulation of the cytotoxic nucleotide intermediate dUTP. These data demonstrate that HDACi repress TS expression at the level of transcription and provides the first evidence suggesting a direct mechanistic link between TS downregulation and the synergistic interaction observed between HDACi and 5-FU. This study provides rationale for the continued clinical evaluation of HDACi in combination with 5-FU-based therapies as a strategy to overcome TS-mediated resistance.

Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine

The peptides derived from envelope proteins have been shown to inhibit the protein-protein interactions in the virus membrane fusion process and thus have a great potential to be developed into effective antiviral therapies. There are three types of envelope proteins each exhibiting distinct structure folds. Although the exact fusion mechanism remains elusive, it was suggested that the three classes of viral fusion proteins share a similar mechanism of membrane fusion. The common mechanism of action makes it possible to correlate the properties of self-derived peptide inhibitors with their activities. Here we developed a support vector machine model using sequence-based statistical scores of self-derived peptide inhibitors as input features to correlate with their activities. The model displayed 92% prediction accuracy with the Matthew’s correlation coefficient of 0.84, obviously superior to those using physicochemical properties and amino acid decomposition as input. The predictive support vector machine model for self- derived peptides of envelope proteins would be useful in development of antiviral peptide inhibitors targeting the virus fusion process.

Flat SAR of P3-methylsulphonamide based small molecule legumain inhibitors

This letter describes the design, development and SAR exploration of a novel series of small legumain inhibitors. The SAR of a new small molecule legumain inhibitor chemotype was explored and found to have improved physiochemical properties compared to previously developed inhibitors within our group. However, further development of this series was found to be limited as the SAR was observed to be relatively flat.

Drug induced gingival overgrowth: A role for Protease Activated Receptors?

Background: Protease activated receptors (PAR) belong to a subfamily of G protein coupled receptors. They consist of seven transmembrane domains but are not classical receptors as their agonist is a circulating serine proteinase. This proteinase cleaves an N-terminal extracellular domain of the receptor to reveal a new N-terminal tethered ligand which binds intramolecularly, thus converting an extracellular proteolytic event into a transmembrane signal. Therefore, the cleavage and activation of PARs provide a mechanism whereby proteinases can directly influence the inflammatory response. Gingival hyperplasia or gingival enlargement is a side effect of some drugs such as cyclosporine, a potent immunosuppressant. To date, the potential role of PAR in the inflammation associated with the pathogenesis of gingival overgrowth has not been studied. Objectives: The present study was designed to determine whether proteinases derived from extracts of cyclosporine induced hyperplasia were capable of activating PAR in vitro. Methods: Cell lysates were derived from tissue obtained from gingival overgrowth of patients requiring surgical excision. Cell lines over-expressing PARs were maintained in Dulbecco's modified Eagle's medium (DMEM), containing 10% foetal calf serum (FCS) in 5% CO2. The cells were treated with gingival overgrowth lysates and agonist stimulated calcium release from the cells was recorded using the Fluo-4-Direct™ Calcium Assay Kit from Invitrogen, according to manufacturer's instructions. Results: Calcium release by activated PAR on tumour cells was detected in those treated with gingival hyperplasia lysates. Samples from healthy gingival fibroblasts did not elicit this response. Conclusions: The identification of mediators of the molecular events central to the inflammatory phenotype elicited by gingival hyperplasia is important. To this end, our experiments show that in vitro, enzymes derived from overgrown gingival tissue are capable of activating PAR and thereby provide evidence for the potential role of PAR in sustaining gingival hyperplasia.

The role of LL-37 in periodontal wound healing

Introduction: As a result of chronic inflammation during periodontal disease the junctional epithelium becomes micro-ulcerated. The inflammatory process is mediated by both bacterial and host cell products. Host defence peptides such as defensins, secretory leucocyte protease inhibitor (SLPI) and the sole human cathelicidin, LL-37, are secreted by both periodontal cells and neutrophils into gingival crevicular fluid (GCF). They have the ability to modulate the immune response in periodontitis and are thought to have a potential role in periodontal wound healing. Objectives: The aims of this study were to determine the role of LL-37 in the production of Interleukin (IL)-8, IL-6, hepatocyte growth factor (HGF) and basic-fibroblast growth factor (bFGF) by gingival fibroblasts. The role of LL-37 in modulating total matrix metalloproteinase (MMP) activity and expression of tissue inhibitors of metalloproteinase (TIMP)-1 and -2 by gingival fibroblasts was also investigated. Methods: Primary gingival fibroblasts were co-cultured with concentrations of LL-37 (1, 5 and 10µg/ml) for 24 hours and their supernatants tested for levels of IL-8 and IL-6, HGF, bFGF, TIMP-1 and TIMP-2 by ELISA. Rates of MMP turnover in the supernatants were tested by fluorogenic assay using fluorescence resonance energy transfer (FRET) peptide substrates. Cytotoxicity was measured by MTT assay. Statistical significance was measured using the independent t-test and p<0.05 was considered significant. Results: LL-37 significantly upregulated levels of IL-8, IL-6, HGF, bFGF and TIMP-1 (p<0.05) in a dose-dependent fashion. LL-37 significantly decreased the total MMP activity (p<0.05). None of the LL-37 concentrations tested were cytotoxic to gingival fibroblasts. Conclusion: These results indicate that LL-37 is involved in periodontal wound healing. LL-37 increased levels of proinflammatory cytokines and increased levels of growth factors involved in re-epithelialisation. LL-37 has the ability to regulate remodelling of the periodontium by controlling MMP overactivity both directly and by stimulating production of inhibitors by gingival fibroblasts.

Protease activated receptor 2 expression and functionality in caries

Introduction: Protease activated receptors (PARs) are G-protein-coupled transmembrane receptors that are expressed on many cell types and implicated in various inflammatory processes in vivo. The induction of PAR2 as a result of the inflammatory response associated with dental caries remains to be determined. Objectives: The aim was to localise the expression of PAR2 in human dental pulp from carious teeth and to confirm receptor functionality using an in vitro assay. Methods: Dental pulp sections from decalcified carious teeth were examined by immunocytochemsitry. Membrane preparations from cultured pulp fibroblasts were subject to SDS-PAGE and immunoblotting to confirm fibroblast-associated immunoreactivity. The functionality of PAR2 on dental pulp fibroblasts was studied using calcium imaging in the presence of several potential activators including a PAR2 agonist (PAR2-AP), trypsin and pulpal enzymes from a carious tooth. Results: Immunocytochemistry revealed intense PAR2 immunoreactivity on pulpal fibroblasts subjacent to carious lesions but not in surrounding regions of the dental pulp. Pulp specimens from a dental injury model showed no expression of PAR2, suggesting its expression was related to cellular changes associated with ongoing caries. The localisation of PAR2 staining to pulpal fibroblasts in carious teeth was confirmed by Western blotting which revealed PAR2 immunoreactive bands in membrane fractions prepared from pulp fibroblasts. In functional studies, challenge of cultured pupal fibroblasts with PAR2-AP, trypsin and an extract of proteolytic enzymes from a carious dental pulp, showed specific activation of PAR2. Conclusions: This work demonstrates that PAR2 is functional and inducible in human dental pulp fibroblasts in response to caries and that endogenous pulpal enzymes can activate PAR2.

Clinical Application of Poly(ADP-Ribose) Polymerase Inhibitors in High-Grade Serous Ovarian Cancer

: High-grade serous ovarian cancer is characterized by genomic instability, with one half of all tumors displaying defects in the important DNA repair pathway of homologous recombination. Given the action of poly(ADP-ribose) polymerase (PARP) inhibitors in targeting tumors with deficiencies in this repair pathway by loss of BRCA1/2, ovarian tumors could be an attractive population for clinical application of this therapy. PARP inhibitors have moved into clinical practice in the past few years, with approval from the Food and Drug Administration (FDA) and European Medicines Agency (EMA) within the past 2 years. The U.S. FDA approval of olaparib applies to fourth line treatment in germline BRCA-mutant ovarian cancer, and European EMA approval to olaparib maintenance in both germline and somatic BRCA-mutant platinum-sensitive ovarian cancer. In order to widen the ovarian cancer patient population that would benefit from PARP inhibitors, predictive biomarkers based on a clear understanding of the mechanism of action are required. Additionally, a better understanding of the toxicity profile is needed if PARP inhibitors are to be used in the curative, rather than the palliative, setting. We reviewed the development of PARP inhibitors in phase I-III clinical trials, including combination trials of PARP inhibitors and chemotherapy/antiangiogenics, the approval for these agents, the mechanisms of resistance, and the outstanding issues, including the development of biomarkers and the rate of long-term hematologic toxicities with these agents.

IMPLICATIONS FOR PRACTICE: The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib has recently received approval from the Food and Drug Administration (FDA) and European Medicines Agency (EMA), with a second agent (rucaparib) likely to be approved in the near future. However, the patient population with potential benefit from PARP inhibitors is likely wider than that of germline BRCA mutation-associated disease, and biomarkers are in development to enable the selection of patients with the potential for clinical benefit from these agents. Questions remain regarding the toxicities of PARP inhibitors, limiting the use of these agents in the prophylactic or adjuvant setting until more information is available. The indications for olaparib as indicated by the FDA and EMA are reviewed.

Active corrosion protection of AA2024 by sol-gel coatings with corrosion inhibitors

A indústria aeronáutica utiliza ligas de alumínio de alta resistência para o fabrico dos elementos estruturais dos aviões. As ligas usadas possuem excelentes propriedades mecânicas mas apresentam simultaneamente uma grande tendência para a corrosão. Por esta razão essas ligas necessitam de protecção anticorrosiva eficaz para poderem ser utilizadas com segurança. Até à data, os sistemas anticorrosivos mais eficazes para ligas de alumínio contêm crómio hexavalente na sua composição, sejam pré-tratamentos, camadas de conversão ou pigmentos anticorrosivos. O reconhecimento dos efeitos carcinogénicos do crómio hexavalente levou ao aparecimento de legislação banindo o uso desta forma de crómio pela indústria. Esta decisão trouxe a necessidade de encontrar alternativas ambientalmente inócuas mas igualmente eficazes. O principal objectivo do presente trabalho é o desenvolvimento de prétratamentos anticorrosivos activos para a liga de alumínio 2024, baseados em revestimentos híbridos produzidos pelo método sol-gel. Estes revestimentos deverão possuir boa aderência ao substrato metálico, boas propriedades barreira e capacidade anticorrosiva activa. A protecção activa pode ser alcançada através da incorporação de inibidores anticorrosivos no prétratamento. O objectivo foi atingido através de uma sucessão de etapas. Primeiro investigou-se em detalhe a corrosão localizada (por picada) da liga de alumínio 2024. Os resultados obtidos permitiram uma melhor compreensão da susceptibilidade desta liga a processos de corrosão localizada. Estudaram-se também vários possíveis inibidores de corrosão usando técnicas electroquímicas e microestruturais. Numa segunda etapa desenvolveram-se revestimentos anticorrosivos híbridos orgânico-inorgânico baseados no método sol-gel. Compostos derivados de titania e zirconia foram combinados com siloxanos organofuncionais a fim de obter-se boa aderência entre o revestimento e o substrato metálico assim como boas propriedades barreira. Testes industriais mostraram que estes novos revestimentos são compatíveis com os esquemas de pintura convencionais actualmente em uso. A estabilidade e o prazo de validade das formulações foram optimizados modificando a temperatura de armazenamento e a quantidade de água usada durante a síntese. As formulações sol-gel foram dopadas com os inibidores seleccionados durante a primeira etapa e as propriedades anticorrosivas passivas e activas dos revestimentos obtidos foram estudadas numa terceira etapa do trabalho. Os resultados comprovam a influência dos inibidores nas propriedades anticorrosivas dos revestimentos sol-gel. Em alguns casos a acção activa dos inibidores combinou-se com a protecção passiva dada pelo revestimento mas noutros casos terá ocorrido interacção química entre o inibidor e a matriz de sol-gel, de onde resultou a perda de propriedades protectoras do sistema combinado. Atendendo aos problemas provocados pela adição directa dos inibidores na formulação sol-gel procurou-se, numa quarta etapa, formas alternativas de incorporação. Na primeira, produziu-se uma camada de titania nanoporosa na superfície da liga metálica que serviu de reservatório para os inibidores. O revestimento sol-gel foi aplicado por cima da camada nanoporosa. Os inibidores armazenados nos poros actuam quando o substrato fica exposto ao ambiente agressivo. Numa segunda, os inibidores foram armazenados em nano-reservatórios de sílica ou em nanoargilas (halloysite), os quais foram revestidos por polielectrólitos montados camada a camada. A terceira alternativa consistiu no uso de nano-fios de molibdato de cério amorfo como inibidores anticorrosivos nanoparticulados. Os nano-reservatórios foram incorporados durante a síntese do sol-gel. Qualquer das abordagens permitiu eliminar o efeito negativo do inibidor sobre a estabilidade da matriz do sol-gel. Os revestimentos sol-gel desenvolvidos neste trabalho apresentaram protecção anticorrosiva activa e capacidade de auto-reparação. Os resultados obtidos mostraram o elevado potencial destes revestimentos para a protecção anticorrosiva da liga de alumínio 2024.

Evaluation of quinazolin-4-piperidine sulfamides as inhibitors of human NPP1: relevance in the treatment of pathologic mineralization of valve interstitial cells

Le rétrécissement valvulaire aortique calcifié (RAC) est le trouble valvulaire le plus fréquent chez les personnes âgées des pays développés. La seule option de traitement possible le remplacement de la valve aortique. L’identification du rôle de l’enzyme ecto-nucleotidase NPP1 dans le processus de calcification suggère que cette enzyme pourrait être une cible potentielle pour le développement d’un inhibiteur pharmacologique contre la calcification de la valve aortique. Jusqu’à présent, les composés qui ont été développés en tant qu’inhibiteurs de NPP1 manquent de puissance et de spécificité. Dans la présente étude, nous avons démontré que les dérivés de sulfonamides quinazolin-4-pipéridine sont des inhibiteurs puissants, spécifiques, et non-compétitifs de NPP1. In vitro, dans des cellules isolées de valve aortique nous avons fourni des preuves que l’inhibition de NPP1 par ces dérivés bloque la minéralisation, l’apoptose et la transition ostéogénique des cellules interstitielles de valve aortique.

Development of user-friendly, high throughput screening for ligands and inhibitors of carbohydrate modifying enzymes

This paper describes the impact of cloud computing and the use of GPUs on the performance of Autodock and Gromacs respectively. Cloud computing was applicable to reducing the ‘‘tail’’ seen in running Autodock on desktop grids and the GPU version of Gromacs showed significant improvement over the CPU version. A large (200,000 compounds) library of small molecules, seven sialic acid analogues of the putative substrate and 8000 sugar molecules were converted into pdbqt format and used to interrogate the Trichomonas vaginalis neuraminidase using Autodock Vina. Good binding energy was noted for some of the small molecules (~-9 kcal/mol), but the sugars bound with affinity of less than -7.6 kcal/mol. The screening of the sugar library resulted in a ‘‘top hit’’ with a-2,3-sialyllacto-N-fucopentaose III, a derivative of the sialyl Lewisx structure and a known substrate of the enzyme. Indeed in the top 100 hits 8 were related to this structure. A comparison of Autodock Vina and Autodock 4.2 was made for the high affinity small molecules and in some cases the results were superimposable whereas in others, the match was less good. The validation of this work will require extensive ‘‘wet lab’’ work to determine the utility of the workflow in the prediction of potential enzyme inhibitors.

A thin-layer chromatography-bioautographic method for detecting dipeptidyl peptidase IV inhibitors in plants

A thin-layer chromatography (TLC)-bioautographic method was developed with the aim to detect dipeptidyl peptidase IV (DPP IV) inhibitors from plant extracts. The basic principle of the method is that the enzyme (DPP IV) hydrolyzes substrate (Gly-Pro-p-nitroaniline) into p-nitroaniline (pNA), which diazotizes with sodium nitrite, and then reacts with N-(1-naphthyl) ethylenediamine dihydrochloride in turn to form a rose-red azo dye which provides a rose-red background on the TLC plates. The DPP IV inhibitors showed white spots on the background as they blocked enzymolysis of the substrate to produce pNA. The method was validated with respect to selectivity, sensitivity, linearity, precision, recovery, and stability after optimizing key parameters including plate type, time and temperature of incubation, concentration of substrate, enzyme and derivatization reagents, and absorption wavelength. The results showed good lineary within amounts over 0.01–0.1 μg range for the positive control, diprotin A, with the coefficient of determination (r2) = 0.9668. The limits of detection (LOD) and quantification (LOQ) were 5 and 10 ng, respectively. The recoveries ranged from 98.9% to 107.5%. The averages of the intra- and inter-plate reproducibility were in the range of 4.1–9.7% and 7.6–14.7%, respectively. Among the nine methanolic extracts of medicinal herbs screened for DPP IV inhibitors by the newly developed method, Peganum nigellastrum Bunge was found to have one white active spot, which was then isolated and identified as harmine. By spectrophotometric method, harmine hydrochloride was found to have DPP-IV inhibitory activity of 32.4% at 10 mM comparing to that of 54.8% at 50 μM for diprotin A.

Construction and evaluation of cysteine selective electrodes for FIA analysis of pharmaceuticals

A flow injection analysis (FIA) system comprising a cysteine selective electrode as detection system was developed for determination of this amino acid in pharmaceuticals. Several electrodes were constructed for this purpose, having PVC membranes with different ionic exchangers and mediator solvents. Better working characteristics were attained with membranes comprising o-nitrophenyl octyl ether as mediator solvent and a tetraphenylborate based ionic-sensor. Injection of 500 µL standard solutions into an ionic strength adjuster carrier (3x10-3 M) of barium chloride flowing at 2.4mL min-1, showed linearity ranges from 5.0x10-5 to 5.0x10-3 M, with slopes of 76.4±0.6mV decade-1 and R2>0.9935. Slope decreased significantly under the requirement of a pH adjustment, selected at 4.5. Interference of several compounds (sodium, potassium, magnesium, barium, glucose, fructose, and sucrose) was estimated by potentiometric selectivity coefficients and considered negligible. Analysis of real samples were performed and considered accurate, with a relative error to an independent method of +2.7%.

Development of novel benzimidazole- based COX Inhibitors new synthetic strategies and screening of heterocyclic structures

Dissertação para obtenção do Grau de Doutor em Química, especialidade Química Orgânica

Expression of protease-activated receptors in arthritic synovial tissues

Clinical and experimental evidence suggests that synovial thrombin formation in arthritic joints is prominent and deleterious, leading to exacerbation of rheumatoid arthritis (RA). In this context, cellular effects of thrombin mediated by the protease-activated receptors (PARs) in arthritic joints may be of paramount significance. Four PARs have now been identified. PAR1, PAR3, and PAR4 can all be activated by thrombin whereas PAR2 is activated by trypsin and few other proteases.We first explored PARs expression in RA synovial tissues. Synovial membranes from 11 RA patients were analyzed for PARs expression by RT-PCR and by immunohistology. PAR4 was found in all the biopsies, whereas the expression of PAR1, PAR 2 and PAR3 was more restricted (8/11, 5/11 and 3/11 respectively). In the arthritic synovial membrane of murine antigen-induced arthritis (AIA) we found coexpression of the four different PARs. Next, we explored the functional importance of PAR1 during AIA in vivo using PAR-1 deficient mice. The phenotype of PAR1-deficient mice (n = 22), based on the analysis of arthritis severity (as measured by 99 m tecnetium uptake, histological scoring and intra-articular fibrin measurements) was similar to that of wild-type mice (n = 24). In addition, the in vivo production of antibodies against mBSA was also similar. By contrast, the mBSA-induced in vitro lymph node cell proliferation was significantly decreased in PAR1-deficient mice as compared with controls. Accordingly, mBSA-induced production of interferon-γ by lymph node cells in culture was significantly decreased in PAR1-deficient mice as compared with controls, whereas opposite results were observed for production of IL-10.