Synthesis, molecular dynamics simulation, and evaluation of biological activity of novel flurbiprofen and ibuprofen-like compounds.

The frequent use of anti-inflammatory drugs and the side effects of existing drugs keep the need for new compounds constant. For this purpose, flurbiprofen and ibuprofen-like compounds, which are frequently used anti-inflammatory compounds in this study, were synthesized and their structures were elucidated. Like ibuprofen and flurbiprofen, the compounds contain a residue of phenylacetic acid. On the other hand, it contains a secondary amine residue. Thus, it is planned to reduce the acidity, which is the biggest side effect of NSAI drugs, even a little bit. The estimated ADME parameters of the compounds were evaluated. Apart from internal use, local use of anti-inflammatory compounds is also very important. For this reason, the skin permeability values of the compounds were also calculated. And it has been found to be compatible with reference drugs. The COX enzyme inhibitory effects of the obtained compounds were tested by in vitro experiments. Compound 2a showed significant activity against COX-1 enzyme with an IC50 = 0.123 + 0.005 µM. The interaction of the compound with the enzyme active site was clarified by molecular dynamics studies.

DNA topoisomerase IIß as a molecular switch in neural differentiation of mesenchymal stem cells.

Two isoforms of DNA topoisomerase II (topo II) have been identified in mammalian cells, named topo IIα and topo IIß. Topo IIα plays an essential role in segregation of daughter chromosomes and thus for cell proliferation in mammalian cells. Unlike its isozyme topo IIα, topo IIß is greatly expressed upon terminal differentiation of neuronal cells. Although there have been accumulating evidence about the crucial role of topo IIß in neural development through activation or repression of developmentally regulated genes at late stages of neuronal differentiation, there have been no reports that analyzed the roles of topo IIß in the neural trans differentiation process of multipotent stem cells. Terminal differentiation of neurons and transdifferentiation of Mesenchymal Stem Cells (MSCs) are two distinct processes. Therefore, the functional significance of topo IIß may also be different in these differentiation systems. MSC transdifferentiation into neuron-like cells represents an useful model to further validate the role of topo IIß in neuronal differentiation. The aim of this study is to evaluate the subset of genes that are regulated in neural transdifferentiation of bone marrow-derived human MSCs (BM-hMSCs) in vitro and find genes related with topo IIß. For this purpose, topo IIß was silenced by specific small interfering RNAs in hMSCs and cells were induced to differentiate into neuron-like cells. Differentiation and silencing of topo IIß were monitored by real-time cell analysis and also expressions of topo II isoforms were analyzed. Change in transcription patterns of genes upon topo IIß silencing was identified by DNA microarray analysis, and apparently genes involved in regulation of several ion channels and transporters, vesicle function, and cell calcium metabolism were particularly affected by topo IIß silencing suggesting that topoIIß silencing can significantly alter the gene expression pattern of genes involved in variety of biological processes and signal transduction pathways including transcription, translation, cell trafficking, vesicle function, transport, cell morphology, neuron guidance, growth, polarity, and axonal growth. It appears that the deregulation of these pathways may contribute to clarify the further role of topo IIß in neural differentiation.

MicroRNA Targeting.

MicroRNAs (miRNAs) are small noncoding elements that play essential roles in the posttranscriptional regulation of biochemical processes. miRNAs recognize and target multiple mRNAs; therefore, investigating miRNA dysregulation is an indispensable strategy to understand pathological conditions and to design innovative drugs. Targeting miRNAs in diseases improve outcomes of several therapeutic strategies thus, this present study highlights miRNA targeting methods through experimental assays and bioinformatics tools. The first part of this review focuses on experimental miRNA targeting approaches for elucidating key biochemical pathways. A growing body of evidence about the miRNA world reveals the fact that it is not possible to uncover these molecules' structural and functional characteristics related to the biological processes with a deterministic approach. Instead, a systemic point of view is needed to truly understand the facts behind the natural complexity of interactions and regulations that miRNA regulations present. This task heavily depends both on computational and experimental capabilities. Fortunately, several miRNA bioinformatics tools catering to nonexperts are available as complementary wet-lab approaches. For this purpose, this work provides recent research and information about computational tools for miRNA targeting research.

MicroRNAs and Heat Shock Proteins in Breast Cancer Biology.

Breast cancer has five major immune types; luminal A, luminal B, HER2, Basal-like, and normal-like. Cells produce a family of protein called heat shock proteins (Hsps) in response to exposure to thermal and other proteotoxic stresses play essential roles in cancer metabolism and this large family shows a diverse set of Hsp involvement in different breast cancer immune types. Recently, Hsp members categorized according to their immune type roles. Hsp family consists of several subtypes formed by molecular weight; Hsp70, Hsp90, Hsp100, Hsp40, Hsp60, and small molecule Hsps. Cancer cells employ Hsps as survival factors since most of these proteins prevent apoptosis. Several studies monitored Hsp roles in breast cancer cells and reported Hsp27 involvement in drug resistance, Hsp70 in tumor cell transformation-progression, and interaction with p53. Furthermore, the association of Hsp90 with steroid receptors and signaling proteins in patients with breast cancer directed research to focus on Hsp-based treatments. miRNAs are known to play key roles in all types of cancer that are upregulated or downregulated in cancer which respectively referred to as oncogenes (oncomirs) or tumor suppressors. Expression profiles of miRNAs may be used to classify, diagnose, and predict different cancer types. It is clear that miRNAs play regulatory roles in gene expression and this work reveals miRNA correlation to Hsp depending on specific breast cancer immune types. Deregulation of specific Hsp genes in breast cancer subtypes allows for identification of new targets for drug design and cancer treatment. Here, we performed miRNA network analysis by recruiting Hsp genes detected in breast cancer subtypes and reviewed some of the miRNAs related to aforementioned Hsp genes.

Achieving the balance: Biphasic effects of genistein on PC-3 cells.

This study examined the response of PC-3 cells to physiological (0.5, 2.5, 5, 10 µM) and pharmacological (50 µM) concentrations of genistein which is a main bioactive compound in soy. Following 48 hr genistein treatment, cell-based assays and genome-wide microarray were performed. It was evidenced that maximal physiologically achievable concentrations of genistein (0.5-10 µM) lead to significant increase in cell viability (p < 0.05) and decrease in migration at 0.5 µM (p = 0.000) and 10 µM (p = 0.001). The highest percentage of apoptotic cells was obtained at 50 µM. Microarray analysis gave the most critical pathways such as cell cycle regulation and proliferation, tumorigenesis, DNA damage and repair, stress response, and apoptosis. Physiological concentrations (≤10 µM) induced activation of CDKs, MAPKs, and RPSKs, while high concentrations of genistein (>10 µM) appeared to have a novel mechanism of action, specifically down-regulating TGF-ß by decreasing specifically SMAD 2/3,4 which are in the downstream TGF-ß signaling cascade. PRACTICAL APPLICATIONS: This study highlights for the first time that maximal physiologically achievable concentrations of genistein (0.5-10 µM) have proliferative effects evidenced by alterations in global gene expression patterns of PC-3 cells. Our results particularly represent a closer examination of dietary genistein consumption for the prevention and/or treatment of cancer that maximal physiologically achievable concentrations of genistein could have detrimental effects on individuals with prostate cancer. Further studies as in vivo would be necessary to remove shadows on the effect of genistein on prostate cancer progression.

Synthesis and antimicrobial activity of 4-phenyl/cyclohexyl-5-(1-phenoxyethyl)-3-[N-(2-thiazolyl)acetamido]thio-4H-1,2,4-triazole derivatives.

The increasing clinical importance of drug-resistant fungal and bacterial pathogens has lent additional urgency to microbiological research and new antimicrobial compound development. For this purpose, new thiazole derivatives of triazoles were synthesized and evaluated for antifungal and antibacterial activity. The reaction of propionic acid hydrazides with various aryl/alkyl isothiocyanates gave thiosemicarbazides which furnished the mercaptotriazoles by alkali cyclization. The 4-phenyl/cyclohexyl-5-(1-phenoxyethyl)-3-[N-(2-thiazolyl)acetamido]thio-4H-1,2,4-triazole derivatives were synthesized by reacting the mercaptotriazoles with 2-chloro-N-(2-thiazolyl)acetamide. The chemical structures of the compounds were elucidated by IR, 1H-NMR, FAB+-MS spectral data. Their antimicrobial activities against Candida albicans (two strains), Candida glabrata, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa were investigated. The results showed that some of the compounds have very strong antifungal activity.

Knockdown of Pin1 leads to reduced angiogenic potential and tumorigenicity in glioblastoma cells.

Glioblastoma is the most common and most aggressive type of primary brain tumor. Current approaches in the treatment of glioblastoma are not effective enough to increase patient survival or prevent recurrence following surgery. Consequently, the search for potential drug targets is ongoing. Peptidyl-prolyl cis/trans isomerase NIMA-interacting 1 (Pin1), an isomerase that is overexpressed in various tumors, has become an attractive molecule in cancer research. Pin1 has been reported to regulate proteins involved in essential cellular pathways that mediate cell proliferation, cell cycle progression, differentiation and apoptosis, by altering their stability and function. The results of the present study revealed that knockdown of Pin1 in glioblastoma cells using RNA interference or the selective Pin1 inhibitor, juglone, suppressed the tumorigenic features by reducing cell growth, migration and angiogenic potential. Furthermore, knockdown of Pin1 decreased the levels of vascular endothelial growth factor and matrix metallopeptidase 9, and also triggered apoptosis. Due to the fundamental roles of Pin1 in promoting tumorigenesis, Pin1 inhibitory molecules, including juglone, or alternative synthetic derivatives hold potential for the development of clinical countermeasures against glioblastoma.

Synthesis of some 2-[(benzazole-2-yl)thioacetylamino]thiazole derivatives and their antimicrobial activity and toxicity.

Some 2-[(benzazole-2-yl)thioacetylamino]thiazole derivatives (III) were synthesized by reacting 4-methyl-2-(chloroacetylamino)thiazole derivatives (I) with benzazol-2-thiole (II) in acetone in the presence of K(2)CO(3). The chemical structures of the compounds were elucidated by (1)H NMR and FAB(+)-MS spectral data. The prepared compounds were tested for antimicrobial activity and toxicity.

In silico identification and characterization of the MAPK family members of unicellular model eukaryote Tetrahymena thermophila.

The biological function and evolutionary diversity of the mitogen-activated protein kinase (MAPK) family have mostly been studied in fungi, animals and plants, with very limited information from lower eukaryotes. This study aimed to describe the MAPKs of unicellular Tetrahymena thermophila. Eight members of the T. thermophila MAPK (TtMPK) gene family, in addition to previously reported TtMPK1, TtMPK2 and TtMPK3, were identified bioinformatically using a T. thermophila genome database. Phylogenetic analysis assigned the TtMPKs into two major groups, ERK1/2-like (TtMPK1, 2, 3, 5, 6, 7, 8, and 9) as stress-responsive MAPKs for biotic and abiotic stresses, and ERK7/8-like (TtMPK4, 10, and 11) as cell-cycle-associated protein kinases for biotic factors. Semi-quantitative RT-PCR analysis of the TtMPKs showed high mRNA expression at 30°C; however, only TtMPK5 and TtMPK6 showed high expression at 37°C. Osmotic shock by 100mM NaCl only increased the expression of TtMPK2, whereas 20mM NaCl reduced the expression of all MPKs to almost zero. The results suggested that T. thermophila MAPKs are among the closest representatives of the ancestors of the eukaryotic MAPK family. Although no functional characterization of MPKs was performed, this study is the first report of the genome-wide MAPK family in T. thermophila.

Cloning, expression and characterization of a gene encoding mitogen activated protein kinase 2 (MPK2) from Tetrahymena thermophila.

Environmental effects and mitogens determine cell phenotype in eukaryotes mainly through MAPK pathways. However, MAPK signaling pathways in T. thermophila have not been studied comprehensively. This study aims to express recombinant MPK2, a MAPK from T. thermophila, in E. coli to characterize its kinase activity. MPK2 was cloned by RT-PCR using degenerate oligonucleotide primers and RACE method. The full-length cDNA of the MPK2 gene is 1705bp that includes 1281bp ORF coding for a putative protein of 426 amino acids having a mass of 50.2kDa. The putative MPK2 protein contains all eleven conserved subdomains that are characteristics of serine/threonine protein kinases, and a TDY motif, which is a putative dual phosphorylation site common in Protista. MPK2 displays highest 48% overall identity to human ERK5 (MAPK7). The expression vector pGEX4T-1-MPK2 was constructed by inserting the coding region of MPK2 cDNA into pGEX4T-1 after introducing the nine point mutations, and then transformed into E. coli BL21(DE3). Autophosphorylation of 76kDa GST-MPK2 at tyrosine residues was confirmed not only by Western blot using anti-phosphotyrosine monoclonal antibody but also by in vitro kinase assay. GST-MPK2 was also able to phosphorylate the artificial substrate myelin basic protein. This study concludes that the free-living unicellular protist T. thermophila MPK2 has commonly conserved MAPK enzyme features, possibly involved in the regulation of cell survival responding to abiotic or biotic stressors, and the production and movement of haploid gametic nuclei between pairs during conjugation.

Phylogenetic analysis of Helicobacter pylori cagA gene of Turkish isolates and the association with gastric pathology.

BACKGROUND: The cagA gene is one of the important virulence factors of Helicobacter pylori. The diversity of cagA 5' conserved region is thought to reflect the phylogenetic relationships between different H. pylori isolates and their association with peptic ulceration. Significant geographical differences among isolates have been reported. The aim of this study is to compare Turkish H. pylori isolates with isolates from different geographical locations and to correlate the association with peptic ulceration. METHODS: Total of 52 isolates of which 19 were Turkish and 33 from other geographic locations were studied. Gastric antral biopsies collected from 19 Turkish patients (Gastritis = 12, ulcer = 7) were used to amplify the cagA 5' region by PCR then followed by DNA sequencing. RESULTS: The phylogenetic tree displayed 3 groups: A) a mix of 2 sub-groups "Asian" and "African/Anatolian/Asian/European", B) "Anatolian/European" and C) "American-Indian". Turkish H. pylori isolates clustered in the mixed sub-group A were mostly from gastritis patients while those clustered in group B were from peptic ulcer patients. A phylogenetic tree constructed for our Turkish isolates detected distinctive features among those from gastritis and ulcer patients. We have found that 2/3 of the gastritis isolates were clustered alone while 1/3 was clustered together with the ulcer isolates. Several amino acids were found to be shared between the later groups but not with the first group of gastritis. CONCLUSIONS: This study provided an additional insight into the profile of our cagA gene which implies a relationship in geographic locations of the isolates.

Synthesis and antibacterial activity of tert-butyl [1-benzyl-2[(4-aryl-2-thiazolyl)hydrazono]ethyl]carbamate derivatives.

The increasing clinical importance of drug-resistant fungal and bacterial pathogens has lent additional urgency to microbiological research and new antibacterial compound development. For this purpose, new tert-butyl[1-benzyl-2[(4-aryl-2-thiazolyl)hydrazono]ethyl]carbamate derivatives were synthesized and evaluated for antibacterial activity. The reaction of Boc-L-phenylalaninal with thiosemicarbazide gave the thiosemicarbazone which furnished the title compounds by reaction with phenacyl bromides. The newly synthesized compounds were screened for antibacterial activity and toxicity. While microdilution broth susceptibility assay was used for the antibacterial activity evaluation of the compounds against the strains E. coli (NRRL B-3704), M. luteus (NRRL B-4375), B. cereus (NRRL B-3711), P. aeruginosa (NRRL B-23), and S. fecalis (NRRL B-14617), the Artemia salina 96-well assay was used to determine cytotoxicities of the compounds. Observations obtained from the bioassays showed that some of the compounds are highly active against E. coli, M. luteus, and B. cereus when compared with the control agent and showed low toxicity.