In silico structural, phylogenetic and drug target analysis of putrescine monooxygenase from Shewanella putrefaciens-95.

BACKGROUND: The enormous and irresponsible use of antibiotics has led to the emergence of resistant strains of bacteria globally. A new approach to combat this crisis has been nutritional immunity limiting the availability of nutrients to pathogens. Targeting the siderophore biosynthetic pathway that helps in iron acquisition, an essential microelement in the bacterial system has been the topic of interest in recent days that backs the concept of nutritional immunity. Supporting this view, we have chosen to study a key enzyme in the biosynthetic pathway of putrebactin called putrescine monooxygenase (SpPMO) from Shewanella putrefaciens. In our previous study, we co-expressed putrescine monooxygenase recombinantly in Escherichia coli BL21 Star (DE3). The bioinformatic analysis and screening of inhibitors will broaden the scope of SpPMO as a drug target. RESULTS: In the present study, we have analysed the physicochemical properties of the target enzyme and other N-hydroxylating monooxygenases (NMOs) using ExPASy server. The target enzyme SpPMO and most of the selected NMOs have a slightly acidic isoelectric point and are medially thermostable and generally insoluble. The multiple sequence alignment identified the GXGXX(N/A), DXXXFATGYXXXXP motives and conserved amino acids involved in FAD binding, NADP binding, secondary structure formation and substrate binding. The phylogenetic analysis indicated the distribution of the monooxygenases into different clades according to their substrate specificity. Further, a 3D model of SpPMO was predicted using I-TASSER online tool with DfoA from Erwinia amylovora as a template. The model was validated using the SAVES server and deposited to the Protein Model Database with the accession number PM0082222. The molecular docking analysis with different substrates revealed the presence of a putrescine binding pocket made of conserved amino acids and another binding pocket present on the surface of the protein wherein all other ligands interact with high binding affinity. The molecular docking of naturally occurring inhibitor molecules with SpPMO 3D model identified curcumin and niazirin with 1.83 and 2.81 µM inhibition constants as two promising inhibitors. Further studies on kinetic parameters of curcumin and niazirin inhibitors in vitro determined the Ki to be 2.6±0.0036 µM and 18.38±0.008 µM respectively. CONCLUSION: This analysis will help us understand the structural, phylogenetic and drug target aspects of putrescine monooxygenase from Shewanella putrefaciens-95 in detail. It sheds light on the precautionary measures that can be developed to inhibit the enzyme and thereby the secondary infections caused by them.

Preparation and characterization of carrageenan/silver nanoparticles/Laponite nanocomposite coating on oxygen plasma surface modified polypropylene for food packaging.

In this work, the nano composites of carrageenan/AgNPs/Laponite were prepared and coated on the oxygen plasma surface modified polypropylene film to enhance the barrier and adhesion properties. The mechanical, barrier, adhesion and antimicrobial properties were also studied to use for food packaging applications. The polypropylene film was surface modified with oxygen plasma treatment for 60 s. The AgNPs are prepared by green synthesis method from the Digitalis purpurea plant. Then the carrageenan based nanocomposites were coated by roller coating method with the thickness of 24 µm. By using scanning electron microscopy, the morphology of the coating was investigated. The Laponite and AgNPs dispersion was analyzed by X-ray diffraction analysis. The tensile and adhesion strength of the coated film was increased and the OTR and WVTR were decreased after the incorporation of Laponite and AgNPs. It exhibited the strong antimicrobial activity against the E. coli and S. aureus.

Iodine-catalyzed condensation of isatin with indoles: a facile synthesis of di(indolyl)indolin-2-ones and evaluation of their cytotoxicity.

Isatin reacts smoothly with indoles in the presence of a catalytic amount of molecular iodine under mild conditions to afford a novel class of di(indolyl)indolin-2-one derivatives in good yields. These molecules are found to possess a promising cytotoxicity against cancer cells only but not on normal cells.

Iodine-catalyzed conjugate addition of indoles onto en-1,4-dione: a novel synthesis of 3-(1-(1H-indol-3-yl)-2-oxo-2-phenylethyl)indolin-2-ones as antibacterial and antifungal agents.

Indole and its derivatives undergo smooth conjugate addition onto en-1,4-dione derived from isatin and acetophenone, in the presence of a catalytic amount of molecular iodine in acetonitrile under mild conditions to afford a novel class of 3-(1-(1H-indol-3-yl)-2-oxo-2-phenylethyl)indolin-2-one derivatives in good yields with high degree of 1,4-selectivity. Some of these compounds are found to exhibit modest antibacterial and antifungal properties.

Epigenetic changes and their clinical relevance in Saudi diffuse large B-cell lymphoma. A molecular and tissue microarray analysis of 100 cases.

OBJECTIVE: The gene encoding the DNA repair enzyme O6-methylguanine-DNA methyltransferase (MGMT) is transcriptionally silenced by promoter hypermethylation in several human cancers including diffuse large B-cell lymphoma (DLBCL). We explored the aberrant promoter methylation of MGMT in Saudi diffuse large B-cell lymphoma and to investigate MGMT hypermethylation has an effect on patient's overall survival. METHODS: In a retrospective cohort study, 100 cases of DLBCL were collected from the Department of Pathology at King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia. We used methylation specific polymerase chain reaction to analyze the MGMT promoter methylation status in 100 tumor DNA of Saudi DLBCL patients receiving multi drug regimens. Tissue microarray (TMA) of these cases was also constructed. The MGMT protein expression was analyzed immunohistochemically. Molecular data were correlated with clinical outcome. RESULTS: Seventy one percent (71%) of 100 DLBCL patients showed MGMT promoter hypermethylation in their lymphoma. The presence of MGMT methylation was associated with statistically significant increase in the overall survival (p=0.02). The MGMT promoter hypermethylation was independent and a strong prognostic factor. CONCLUSION: The MGMT promoter hypermethylation appears to be useful marker for predicting survival in patient with DLBCL treated with multi drug regimens including cyclophosphamide, at the same time the study shows that TMA technology is useful for immunohistochemical analysis of large lymphoma populations.

Risk assessment in first degree female relatives of breast cancer patients using the alkaline Comet assay.

First degree female relatives (FDFRs) of breast cancer patients have been reported to have a 2- to 3-fold increase in breast cancer risk as compared with the general population. Assessment of genetic instability (DNA damage and repair efficiency) is an important parameter concerning mutagenesis and carcinogenesis. In an attempt to identify individuals at high risk of breast cancer in the FDFRs of breast cancer patients, two tests were used: the alkaline Comet assay on leucocytes and the micronucleus test (MNT) on buccal epithelial cells. In addition to FDFRs, two other categories of subjects were included: breast cancer patients and controls. The Comet assay was used to study basal DNA damage, DNA susceptibility to a mutagen (N-methyl N-nitro N-nitrosoguanidine) and DNA repair efficiency. In addition, the MNT served as an indicator of chromosome breakage/aneuploidy. A significant increase in DNA damage (basal and after treatment with a mutagen, as well as after allowing repair to take place) and micronucleus frequency was observed from controls to FDFRs and from FDFRs to breast cancer patients. There was considerable variability in the subjects with respect to both of these parameters. Outliers identified among the FDFRs based on 3 SD limits of DNA damage and micronucleus frequency were considered as high risk individuals.

Risk assessment in cervical dysplasia patients by single cell gel electrophoresis assay: a study of DNA damage and repair.

Precancerous lesions of cervix, commonly known as dysplasia, present a complex problem because of their biological behavior. Increased genetic instability, either inherent or induced by some external mutagen, is considered as a primary event or a predisposing factor to neoplastic transformation. The relationship between genetic instability and susceptibility towards cervical cancer was evaluated with the comet or single cell gel electrophoresis (SCGE) assay. Among precancerous individuals, genomic instability was observed in cervical epithelial cells and peripheral blood leukocytes. The mean basal DNA damage and mean susceptibility to DNA damage by the mutagen (MNNG) treatment increased whereas repair capacity decreased with progression of the disease in a stepwise manner. Inter and intra individual variability was maximum in cancerous group. Risk was estimated by giving a predictive value for each precancerous individual. In combination with morphological, biochemical, and cytogenetic parameters, the SCGE assay may serve as a novel tool to predict the fate of cervical dysplasia.