Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria

BACKGROUND: Drug resistance to anti-malarial compounds remains a serious problem, with resistance to newer pharmaceuticals developing at an alarming rate. The development of new anti-malarials remains a priority, and the rational selection of putative targets is a key element of this process. Discovery-2 is an update of the original Discovery in silico resource for the rational selection of putative drug target proteins, enabling researchers to obtain information for a protein which may be useful for the selection of putative drug targets, and to perform advanced filtering of proteins encoded by the malaria genome based on a series of molecular properties. METHODS: An updated in silico resource has been developed where researchers are able to mine information on malaria proteins and predicted ligands, as well as perform comparisons to the human and mosquito host characteristics. Protein properties used include: domains, motifs, EC numbers, GO terms, orthologs, protein-protein interactions, protein-ligand interactions. Newly added features include drugability measures from ChEMBL, automated literature relations and links to clinical trial information. Searching by chemical structure is also available. RESULTS: The updated functionality of the Discovery-2 resource is presented, together with a detailed case study of the Plasmodium falciparum S-adenosyl-L-homocysteine hydrolase (PfSAHH) protein. A short example of a chemical search with pyrimethamine is also illustrated. CONCLUSION: The updated Discovery-2 resource allows researchers to obtain detailed properties of proteins from the malaria genome, which may be of interest in the target selection process, and to perform advanced filtering and selection of proteins based on a relevant range of molecular characteristics

Transcriptomic Analysis in Diabetic Nephropathy of Streptozotocin-Induced Diabetic Rats

Diabetic nephropathy (DN) is a major complication of diabetes and is caused by an imbalance in the expression of certain genes that activate or inhibit vital cellular functions of kidney. Despite several recent advances, the pathogenesis of DN remains far from clear, suggesting the need to carry out studies identifying molecular aspects, such as gene expression, that could play a key role in the development of DN. There are several techniques to analyze transcriptome in living organisms. In this study, the suppression subtractive hybridization (SSH) method was used to generate up- and down-regulated subtracted cDNA libraries in the kidney of streptozotocin (STZ)-induced diabetic rats. Northern-blot analysis was used to confirm differential expression ratios from the obtained SSH clones to identify genes related to DN. 400 unique SSH clones were randomly chosen from the two subtraction libraries (200 of each) and verified as differentially expressed. According to blast screening and functional annotation, 20.2% and 20.9% of genes were related to metabolism proteins, 9% and 3.6% to transporters and channels, 16% and 6.3% to transcription factors, 19% and 17.2% to hypothetical proteins, and finally 24.1 and 17.2% to unknown genes, from the down- and up-regulated libraries, respectively. The down- and up-regulated cDNA libraries differentially expressed in the kidney of STZ diabetic rats have been successfully constructed and some identified genes could be highly important in DN

Childhood rhabdomyosarcoma metastatic to bone marrow presenting with disseminated intravascular coagulation and acute tumour lysis syndrome: review of the literature apropos of two cases

The paper presents diagnostic and therapeutic difficulties in two adolescents with widespread rhabdomyosarcoma (RMS) presenting with severe haemorrhages resulting from disseminated intravascular coagulation (DIC) and with laboratory features of acute tumour lysis syndrome (ATLS). Other published cases of childhood RMS with DIC at admission have been listed and reviewed. It has been concluded that the clinical picture of a widespread RMS in children may resemble acute hematologic malignancy and pose a big diagnostic problem. That is why the presence of small blue round cells morphologically similar to lymphoblasts and/or myeloblasts in bone marrow (BM), lacking hematopoietic makers, should prompt the pathologist to consider possible diagnosis of RMS. Inclusion of desmin, MyoD1 and myogenin Myf4 to the immunohistochemical panel is obligatory in such cases. When the representative histopathological tumour specimens are difficult to obtain, the flow cytometric immunophenotyping of BM metastases could help the standard morphological/immunohistological diagnostic procedures and advance the diagnosis. Recently, the flow cytometric CD45− CD56+ immunophenotype together with Myf4 transcript has been assigned to RMS cells infiltrating BM. In children with disseminated RMS complicated with DIC rapid polychemotherapy aimed at diminishing the malignancy-triggered procoagulant activity should be initiated. However, in cases with concomitant ATLS the initial doses of chemotherapy should be reduced and the metabolic disorders and renal function monitored. The prognosis in children with RMS metastatic to BM with signs of DIC or ATLS at admission depends on the response to chemotherapy, however generally it is highly disappointing

Homology-based in silico identification of putative protein-ligand interactions in the malaria parasite

Malaria is still one of the most proli c communicable diseases in the world with more than 200 million infections annually, its greatest e ect is felt in the poor nations with-in sub-saharan Africa and south-east Asia. It is especially fatal for women and children where out of the 660 000 fatalities in 2010, 86% were below the age of 5. In the past decade the global fatality rate due to malaria has been signi cantly reduced, primarily due to proliferation of vector control using treated nets and indoor residual spraying of DDT. There have, however, been few innovations in anti-malarial therapeutics and with the threat of the spread of drug resistant strains a need still exists to develop novel drugs to combat malaria infections. One of the major hinderances to drug development is the huge cost of the drug development process, where candidate failures late in development are extremely costly. This is where post-genomic information has the potential of adding great value. By using all available data pertaining to a disease, one gains higher discerning power to select good drug candidates and identify risks early in development before serious investments are made. This need provided the motivation for the development of Discovery; a tool to aid in the identi cation of protein targets and viable lead compounds for the treatment of malaria. Discovery was developed at the University of Pretoria to be a platform for a large spectrum of biological data focused on the malaria causing Plasmodium parasite. It conglomerates various data types into a web-based interface that allows searching using logical lters or by using protein or chemical start points. In 2010 it was decided to rebuild Discovery to improve it's functionality and optimize query times. Also, since its inception various new datasources became available speci cally related to bio-active molecules, these include the ChEMBL database and TCAMS dataset of bio-active molecules and the focus of this project was the integration of said datasets into Discovery. Large quantities of high quality bioactivity data have never been available in the public domain and this has opened up the opportunity to gain even greater insight into the activity of chemical compounds in malaria. Due to conserved structural/functional similarities of proteins between di erent species it is possible to derive predictions about a malaria protein or a chemicals activity in malaria due to experiments carried out on other organisms. These comparisons can be leveraged to highlight potential new compounds that were previously not considered or prevent wasting resources persuing potential compounds that pose threats of toxicity to humans. This project has resulted in a web based system that allows one to search through the chemical space of the malaria parasite. Allowing them to view sets of predicted protein-ligand interactions for a given protein based on that proteins similarity to those existing in the bio-active molecule databases.Dissertation (MSc)--University of Pretoria, 2014.gm2014Biochemistryunrestricte

Hepatocyte Nuclear Factor 1α Proinflammatory Effect Linked to the Overexpression of Liver Nuclear Factor–κB in Experimental Model of Chronic Kidney Disease

Chronic kidney disease (CKD) is associated with low-grade inflammation that activates nuclear factor–κB (NF–κB), which upregulates the expression of numerous NF–κB responsive genes, including the genes encoding IL-6, ICAM-1, VCAM-1, and MCP-1. Herein, we found the coordinated overexpression of genes encoding RelA/p65 (a subunit of NF–κB) and HNF1α in the livers of chronic renal failure (CRF) rats—an experimental model of CKD. The coordinated overexpression of RelA/p65 and HNF1α was associated with a significant increase in IL-6, ICAM-1, VCAM-1, and MCP-1 gene expressions. A positive correlation between liver RelA/p65 mRNA levels and a serum concentration of creatinine and BUN suggest that RelA/p65 gene transcription is tightly related to the progression of renal failure. The knockdown of HNF1α in the HepG2 cell line by siRNA led to a decrease in Rel A/p65 mRNA levels. This was associated with a decrease in IL-6, ICAM-1, VCAM-1, and MCP-1 gene expressions. The simultaneous repression of HNF-1α and RelA/p65 by clofibrate is tightly associated with the downregulation of IL-6, ICAM-1, VCAM-1, and MCP-1 gene expression. In conclusion, our findings suggest that NF–κB could be a downstream component of the HNF1α-initiated signaling pathway in the livers of CRF rats