Genome sequencing projects has led to an explosion of large amount of gene products in which many are of hypothetical proteins with unknown function. Analyzing and annotating the functions of hypothetical proteins is important in Staphylococcus aureus which is a pathogenic bacterium that cause multiple types of diseases by infecting various sites in humans and animals. In this study, ten hypothetical proteins of Staphylococcus aureus were retrieved from NCBI and analyzed for their structural and functional characteristics by using various bioinformatics tools and databases. The analysis revealed that some of them possessed functionally important domains and families and protein-protein interacting partners which were ABC transporter ATP-binding protein, Multiple Antibiotic Resistance (MAR) family, export proteins, Helix-Turn-helix domains, arsenate reductase, elongation factor, ribosomal proteins, Cysteine protease precursor, Type-I restriction endonuclease enzyme and plasmid recombination enzyme which might have the same functions in hypothetical proteins. The structural prediction of those proteins and binding sites prediction have been done which would be useful in docking studies for aiding in the drug discovery.

Background: Superantigens of Staphylococcus aureus namely enterotoxin A, exfoliative toxin A, and Toxic shock syndrome toxin-1 cause detrimental effects on the cells of the immune system. Methods: In this work, the toxins were downloaded from the Protein DataBank database and energies were minimized using KoBaMIN server. Forty flavonoids compounds were identified by pubchem compound database through extensive literature study and their 3D structures were obtained by submitting SMILES to CORINA tool. Based on Lipinski’s rule of five, the molecules were filtered that resulted in 27 compounds. Molecular docking was performed for identifying the binding and interaction sites of flavonoids with the toxins using Autodock 4. Results and Conclusion: The docked complexes were then subjected to molecular dynamics simulation using Gromacs. The analysis revealed the stability of the complexes as indicated by three hydrogen bonds formed during the simulation time period of 20 ns.

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BCR gene is expressed in patients with Philadelphia-positive Leukemias, known as chronic myeloid leukaemia (CML). Here, we focus on how the intramolecular domains and transmembrane segments are involved in the mutated sites of BCR. In this research work, we thoroughly analysed the transmembrane segments and the functional domains and predicted the 3D structure. We applied two kinds of techniques in our work. One is sequence-based, where we proved that the transmembrane segments in the functional domains contain the mutated sites. The second technique is structure-based, where we predicted the 3D structure of BCR gene-coded protein and visualised the transmembrane segments, which included the mutated sites. By using advanced molecular visualisation tools, the molecular structural properties of the respective transmembrane regions of amino acids will be determined. Both the techniques involved the use of advanced insilico tools and database. Our results elucidated that both the sequence and structure-based outcomes represented the identified transmembrane segments in the functional domains, which are potential candidates for drug docking studies. Hence, we finally concluded that this research work would play a vital role in clinical oncology and structure-based drug designing. Our research work is the first attempt to prove that potential drug binding sites are present in BCR oncogene-protein using insilico techniques. The results of this research investigation form a basic foundation for structure-based drug designing.

Recent investigations have rapidly added crucial new insights into the complex functions of the normal BCR gene and of the BCR-ABL chimaera. They are yielding potential therapeutic breakthroughs in the treatment of Philadelphia (Ph) chromosome-positive leukemias. The objective of the present in silico research investigation is to find out whether the functional part (beta-turns) is present in the mutated amino acids of BCR (Breakpoint cluster region) protein. Two significant steps are involved in this study. First, we performed protein sequence modeling of BCR using automated protein modeling servers and the 3D structure was visualized using molecular visualization software and tools. In the second step, the function domains and motifs regions of BCR gene-coded protein is predicted using “PDBsum generate” tool in order to show where exactly the beta-turns lie on the clinically-proven mutated amino acids of BCR protein. The results of our investigation can be used as potential drug binding sites in the field of drug docking studies. It can act as a potential therapeutic agent for Chronic Myeloid Leukemia (CML) type of Leukemia.