Identification and Analysis of Putative Promoter Motifs in Bovine Herpes Virus.
Identification and analysis of putative promoter motifs in bovine herpes virus.
Filed under: Drug and Alcohol Rehabilitation
Bioinformation. 2012; 8(23): 1167-70
Kurjogi MM, Sanakal RD, Kaliwal BB
The purpose of this study is to identify and analyse the putative promoter motifs in the bovine herpes virus which causes several diseases in cattle worldwide including bovine mastitis with large economic impact on dairy industry. Bovine mastitis caused due to virus is often neglected as bacterial infections are held mainly responsible for the disease. Therefore, in this in silico investigation with all the existing experimental data a total of 147 promoter were identified along with their sequences from three genome viz bovine herpes virus 1 (BHV), bovine herpes virus 4 and bovine herpes virus 5, out of which 39 promoters were from bovine herpes virus 4 (BHV 4), 95 from BHV1 and 13 from BHV5 and it was observed that BHV1 and BHV5 have a close evolutionary history. However, they belong to the same subfamily and size of the genome and GC% of BHV1 and BHV5 was almost equal and very high compare to that of BHV4. This analysis may help in designing the live attenuated vaccine against BHV causing bovine mastitis that reduces the incidence of bovine mastitis. Identification of promoters may also help in designing of expression vectors which help in better understanding of the regulation of gene expression. In the era of large genomics and proteomics prediction of promoters in the whole genome is crucial for the advancement of drug discovery and gene therapy.
HubMed – drug
Molecular modeling, docking and ADMET studies towards development of novel Disopyramide analogs for potential inhibition of human voltage gated sodium channel proteins.
Filed under: Drug and Alcohol Rehabilitation
Bioinformation. 2012; 8(23): 1139-46
Meraj K, Mahto MK, Christina NB, Desai N, Shahbazi S, Bhaskar M
The sodium “channelopathies” are the first among the ion channel diseases identified and have attracted widespread clinical and scientific interests. Human voltage gated sodium channels are sites of action of several antiarrhythmic drugs, local anesthetics and related antiepileptic drugs. The present study aims to optimize the activity of Disopyramide, by modification in its structures which may improve the drug action by reducing its side effects. Herein, we have selected Human voltage-gated sodium channel protein type 5 as a potent molecular target. Nearly eighty analogs of Disopyramide are designed and optimized. Thirty are selected for energy minimization using Discovery studio and the LigPrep 2.5. Prior to docking, the active sites of all the proteins are identified. The processing, optimization and minimization of all the proteins is done in Protein preparation wizard. The docking study is performed using the GLIDE. Finally top five ranked lead molecules with better dock scores are identified as having strong binding affinity to 2KAV protein than Disopyramide based on XP G scores. These five leads are further docked with other similar voltage gated sodium channel proteins (PDB IDs: 2KBI, 4DCK, 2L53 and 4DJC) and the best scoring analog with each protein is identified. Drug likeliness and comparative bioactivity analysis for all the analogs is done using QikProp 3.4. Results have shown that the top five lead molecules would have the potential to act as better drugs as compared to Disopyramide and would be of interest as promising starting point for designing compounds against various Sodium channelopathies.
HubMed – drug
Network biology approach for identifying key regulatory genes by expression based study of breast cancer.
Filed under: Drug and Alcohol Rehabilitation
Bioinformation. 2012; 8(23): 1132-8
Chand Y, Alam MA
The use of high-throughput array technology is omnipresent in diverse areas specifically, early diagnosis of disease, discovery of infectious agents, search for biological markers and screening of potential drug candidates. Here, we integrated gene expression data with the network-based approach to identify novel genes that were playing central role in the network through interconnecting to a number of differentially expressed breast cancer genes. The 62 cancerous genes retrieved from the Breast Cancer Gene Database (BCGD) were mapped in the normalized data accessed from Stanford Microarray Database (SMD) to analyze their pattern. Interaction networks for each gene were constructed to understand the biology of the metastasis at systems level. The individual networks were fused together for the detection of interacting hubs, 38 novel genes were found to be deeply intermingled with the central hub node. Gene Ontology studies were made to depict the biology of the hub nodes not alone through gene ranking but by applying the Hyper geometric test with the Benjamini Hochberg False Discovery Rate (FDR) correction method at a significance level of 0.05. Analyzing p-values from the statistical test indicated that most of the novel genes were involved in the same biological function as the disordered genes like signal transducer, transcription regulator, enzyme binding, molecular transducer and receptor signaling protein activity and same pathway as MAPK signaling, Apoptosis, Wnt Signaling, ErbB signaling and Cell Cycle. Lastly, we identified 3 novel genes CHUK, INSR and CREBBP showing high connections with the 12 novel genes reported in literatures as well with the perturbed genes. As a result, these genes can be considered as significant finding in revealing the basis and pathways responsible for breast cancer.
HubMed – drug
Identification of small molecule inhibitors against UBE2C by using docking studies.
Filed under: Drug and Alcohol Rehabilitation
Bioinformation. 2012; 8(21): 1047-58
Sabitha K, Rajkumar T
An increased expression of UBE2C (Ubiquitin-conjugating enzyme E2C) has been associated with high tumor grade and cancer progression. It is an essential indicator of the mitotic destruction events. Our microarray study on cervical cancers showed UBE2C to be over expressed in cervical cancer. Subsequent studies from our laboratory, showed that inhibition of UBE2C can enhance radiation and chemosensitivity. Therefore it can be an appropriate target for drug development to identify potential and specific inhibitor of cancer. To identify small molecule inhibitors, a computational approach was used to model UBE2C and further docking studies were carried out. Different ligand subsets such as ChemBank, PDB, KEGG, Drug-likeness NCI, Not annotated NCI of ligand library ligands were downloaded and docked with UBE2C. Schrodinger tools were used for identifying active sites and docking studies of ligands with UBE2C. Based on glide score, the potential ligands were screened and its interaction with UBE2C was identified. We also analyzed the drug like properties such as absorption, distribution, metabolism, excretion and toxicity (ADME/T) of docked compounds. Our results suggest that 2,4-diimino-1-methyl-1,3,5-triazepan-6-one, sulfuric acid compound with 5,6-diamino-2,4-pyrimidinediol (1:1) and 7-alpha-d-ribofuranosyl-2-aminopurine-5′-phosphate may act as best inhibitors and further in vitro studies, may lead to development of novel and best inhibitor of UBE2C.
HubMed – drug
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