A novel approach to cyclin-dependent kinase 5/p25 inhibitors: A potential treatment for Alzheimer's disease

Based on the earlier results of our in-house database and compound library, a series of novel clubbed thienyl triazoles was designed which may emerge as potential cdk5/p25 inhibitors, for the treatment of Alzheimer's disease. A benign synthesis was planned so as to take an advantage of MAOS (Microwave Assisted Organic Synthesis) method. Evaluation of the SAR of this series has allowed the identification of compounds 4, 5, 7 and 8 from series I while 13, 14, 16 and 17 from series II as significant cdk5/p25 inhibitors and thus have potential as possible treatments for Alzheimer's disease.     

T-iDT : tool for identification of drug target in bacteria and validation by Mycobacterium tuberculosis

With the completion of the Human Genome Project in 2003, many new projects to sequence bacterial genomes were started and soon many complete bacterial genome sequences were available. The sequenced genomes of pathogenic bacteria provide useful information for understanding host-pathogen interactions. These data prove to be a new weapon in fighting against pathogenic bacteria by providing information about potential drug targets. But the limitation of computational tools for finding potential drug targets has hindered the process and further experimental analysis. There are many in silico approaches proposed for finding drug targets but only few have been automated. One such approach finds essential genes in bacterial genomes with no human homologue and predicts these as potential drug targets. The same approach is used in our tool. T-iDT, a tool for the identification of drug targets, finds essential genes by comparing a bacterial gene set against DEG (Database of Essential Genes) and excludes homologue genes by comparing against a human protein database. The tool predicts both the set of essential genes as well as potential target genes for the given genome. The tool was tested with Mycobacterium tuberculosis and results were validated. With default parameters, the tool predicted 236 essential genes and 52 genes to encode potential drug targets. A pathway-based approach was used to validate these potential drug target genes. The pathway in which the products of these genes are involved was determined. Our analysis shows that almost all these pathways are very essential for the bacterial survival and hence these genes encode possible drug targets. Our tool provides a fast method for finding possible drug targets in bacterial genomes with varying stringency level. The tool will be helpful in finding possible drug targets in various pathogenic organisms and can be used for further analysis in novel therapeutic drug development. The tool can be downloaded from http://www.milser.co.in/research.htm and http://www.srmbioinformatics.edu.in/ forum.htm.     

Redox Modulation of Oligomeric State in Proline Utilization A

Homooligomerization of proline utilization A (PutA) bifunctional flavoenzymes is intimately tied to catalytic function and substrate channeling. PutA from Bradyrhizobium japonicum (BjPutA) is unique among PutAs in that it forms a tetramer in solution. Curiously, a dimeric BjPutA hot spot mutant was previously shown to display wild-type catalytic activity despite lacking the tetrameric structure. These observations raised the question of what is the active oligomeric state of BjPutA. Herein, we investigate the factors that contribute to tetramerization of BjPutA in vitro. Negative-stain electron microscopy indicates that BjPutA is primarily dimeric at nanomolar concentrations, suggesting concentration-dependent tetramerization. Further, sedimentation-velocity analysis of BjPutA at high (micromolar) concentration reveals that although the binding of active-site ligands does not alter oligomeric state, reduction of the flavin adenine dinucleotide cofactor results in dimeric protein. Size-exclusion chromatography coupled with multiangle light scattering and small-angle x-ray scattering analysis also reveals that reduced BjPutA is dimeric. Taken together, these results suggest that the BjPutA oligomeric state is dependent upon both enzyme concentration and the redox state of the flavin cofactor. This is the first report, to our knowledge, of redox-linked oligomerization in the PutA family.     

Prevalence of duodenal ulcer-promoting gene (dupA) of Helicobacter pylori in patients with duodenal ulcer in North Indian population

BACKGROUND: The duodenal ulcer (DU)-promoting gene (dupA) of Helicobacter pylori has been identified as a novel virulent marker associated with an increased risk for DU. The presence or absence of dupA gene of H. pylori present in patients with DU and functional dyspepsia in North Indian population was studied by polymerase chain reaction (PCR) and hybridization analysis. MATERIALS AND METHODS: One hundred and sixty-six patients (96 DU and 70 functional dyspepsia) were included in this study. In addition, sequence diversity of dupA gene of H. pylori found in these patients was analyzed by sequencing the PCR products jhp0917 and jhp0918 on both strands with appropriate primers. RESULTS: PCR and hybridization analyses indicated that dupA gene was present in 37.5% (36/96) of H. pylori strains isolated from DU patients and 22.86% (16/70) of functional dyspepsia patients (p < or = .05). Of these, 35 patients with DU (97.2%) and 14 patients with functional dyspepsia (81.25%) were infected by H. pylori positive for cagA genotype. Furthermore, the presence of dupA was significantly associated with the cagA-positive genotype (p < or = .02). CONCLUSION: Results of our study have shown that significant association of dupA gene with DU in this population. The dupA gene can be considered as a novel virulent marker for DU in this population.     

Isolation of microbes associated with field-collected populations of the egg parasitoid,Trichogramma chilonis capable of enhancing biotic fitness

Four bacterial and one yeast species, cultured and identified as Stenotrophomonas maltophilia, Acinetobacter sp., Pseudomonas sp. and Ochrobactrum sp. and the yeast as Metschnikowia reukaufii, were isolated from the internal organs of four collections of field-sourced egg parasitoid, Trichogramma chilonis, obtained as parasitised Helicoverpa armigera eggs. Bacteria were identified through 16 rRNA amplification and sequencing. The single species of yeast was identified through internal transcribed spacer sequences. A single bacterial species could be isolated from each of the four T. chilonis collections; however, all four T. chilonis collections yielded the yeast, M. reukaufii. In order to study the influence of the association of each of the bacterial species and the yeast, microbe-free laboratory-bred populations of T. chilonis were fed with the individual cultures and fitness parameters as parasitisation vigour and female bias were studied in T. chilonis over 10 generations. T. chilonis fed with either S. maltophilia or Acinetobacter sp. and Pseudomonas sp. showed a mean percent increase in female ratio of 26.2%, 30% and 30.3% and mean percent parasitisation of H. armigera eggs significantly increased by 38%, 32.2% and 31.3%, respectively. However, T. chilonis fed with Acinetobacter sp. did not positively influence the two T. chilonis fitness factors. The ubiquitous yeast, M. reukaufii, which could be isolated from all four collections of T. chilonis, could significantly increase both female count and percent parasitism ratio by 22% and 65%, respectively. This study has opened the possibility of modulating the parasitisation fitness of laboratory-bred T. chilonis, prior to field release, using microbes associated with them in the wild.