A bioinformatics approach to characterize a hypothetical protein Q6S8D9_SARS of SARS-CoV.

Characterization as well as prediction of the secondary and tertiary structure of hypothetical proteins from their amino acid sequences uploaded in databases by in silico approach are the critical issues in computational biology. Severe acute respiratory syndrome-associated coronavirus (SARS-CoV), which is responsible for pneumonia alike diseases, possesses a wide range of proteins of which many are still uncharacterized. The current study was conducted to reveal the physicochemical characteristics and structures of an uncharacterized protein Q6S8D9_SARS of SARS-CoV. Following the common flowchart of characterizing a hypothetical protein, several sophisticated computerized tools e.g., ExPASy Protparam, CD Search, SOPMA, PSIPRED, HHpred, etc. were employed to discover the functions and structures of Q6S8D9_SARS. After delineating the secondary and tertiary structures of the protein, some quality evaluating tools e.g., PROCHECK, ProSA-web etc. were performed to assess the structures and later the active site was identified also by CASTp v.3.0. The protein contains more negatively charged residues than positively charged residues and a high aliphatic index value which make the protein more stable. The 2D and 3D structures modeled by several bioinformatics tools ensured that the proteins had domain in it which indicated it was functional protein having the ability to trouble host antiviral inflammatory cytokine and interferon production pathways. Moreover, active site was found in the protein where ligand could bind. The study was aimed to unveil the features and structures of an uncharacterized protein of SARS-CoV which can be a therapeutic target for development of vaccines against the virus. Further research are needed to accomplish the task.

Assessment of antioxidant, anticancer and antimicrobial activity of two vegetable species of Amaranthus in Bangladesh.

BACKGROUND: Amaranthus (Amaranthaceae) has previously been reported to possess different bioactive phytochemicals including phenols, tannins and flavonoids. The current study was designed to evaluate the antioxidant, anti-proliferative and antimicrobial activity of stem and seed extracts of Amaranthus lividus (AL) and Amaranthus hybridus (AH), respectively. METHODS: Antioxidant activity of methanol extract was assessed by DPPH radical scavenging assay. Determination of lectin activity of Amaranthus extract was carried out using hemagglutination assay on mouse blood. A total of thirty six Swiss albino mice containing Ehrlich's ascites carcinoma (EAC) cells were treated with AL and AH extract at 25, 50 and 100 µg/ml/day/mouse for six days. Growth inhibitory activity was determined by haemocytometer counting of EAC cells using trypan blue dye and DAPI (4΄,6-diamidino-2-phenylindole) staining was used to assess apoptotic cells. Gene amplification study was conducted to observe the expression pattern of p53, Bax, Bcl-2 and caspase-3 mRNA using PCR (polymer chain reaction) technique. In vitro susceptibility of five pathogenic bacteria including Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Salmonella typhi and Staphylococcus aureus was detected using disk diffusion assay. RESULTS: The radical scavenging assay indicated that AH and AL possesses potent antioxidant potential, exhibiting IC50 value of 28 ± 1.5 and 93 ± 3.23 µg/ml, respectively. Hemagglutination assay revealed that AH and AL agglutinated mice blood at 1.565 and 3.125 µg/wall, respectively. Administration of AH and AL extract led to 45 and 43 % growth inhibition of EAC cells, respectively at 100 µg/ml with marked features of apoptosis including cell shrinkage, condensation of cytoplasm and aggregation of apoptotic bodies etc. Up-regulation of p53, Bax and caspase-3 and down-regulation of Bcl-2 mRNA in Amaranthus treated mice indicated mitochondria mediated apoptosis of EAC cells in comparison with control. None of the bacterial species showed susceptibility to the extract of both the Amaranthus species. CONCLUSION: Our current findings suggest that both of the Amaranthus species have strong antioxidant, lectin and anti-proliferative activity on EAC cells. The current anticancer potential was observed due mainly to the mitochondria mediated apoptosis of EAC cells.