Identification of putative drug targets in Vancomycin-resistant Staphylococcus aureus (VRSA) using computer aided protein data analysis

• Published in: Gene 2016-01, Vol.575 (1), p.132-143
• Main Authors: Hasan, Md. Anayet, Khan, Md. Arif, Sharmin, Tahmina, Hasan Mazumder, Md. Habibul, Chowdhury, Afrin Sultana
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - antagonists & inhibitors; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Databases, Protein; Drug Delivery Systems; Drug target; Genome subtraction; Humans; Metabolic pathway; Network analysis; Sequence Analysis, Protein; Staphylococcal Infections - drug therapy; Staphylococcal Infections - genetics; Staphylococcal Infections - metabolism; Staphylococcus aureus; Staphylococcus aureus - genetics; Staphylococcus aureus - metabolism; Vancomycin Resistance - genetics; VRSA
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2015.08.044

Vancomycin-resistant Staphylococcus aureus (VRSA) is a Gram-positive, facultative aerobic bacterium which is evolved from the extensive exposure of Vancomycin to Methicillin resistant S. aureus (MRSA) that had become the most common cause of hospital and community-acquired infections. Due to the emergence of different antibiotic resistance strains, there is an exigency to develop novel drug targets to address the provocation of multidrug-resistant bacteria. In this study, in-silico genome subtraction methodology was used to design potential and pathogen specific drug targets against VRSA. Our study divulged 1987 proteins from the proteome of 34,549 proteins, which have no homologues in human genome after sequential analysis through CD-HIT and BLASTp. The high stringency analysis of the remaining proteins against database of essential genes (DEG) resulted in 169 proteins which are essential for S. aureus. Metabolic pathway analysis of human host and pathogen by KAAS at the KEGG server sorted out 19 proteins involved in unique metabolic pathways. 26 human non-homologous membrane-bound essential proteins including 4 which were also involved in unique metabolic pathway were deduced through PSORTb, CELLO v.2.5, ngLOC. Functional classification of uncharacterized proteins through SVMprot derived 7 human non-homologous membrane-bound hypothetical essential proteins. Study of potential drug target against Drug Bank revealed pbpA-penicillin-binding protein 1 and hypothetical protein MQW_01796 as the best drug target candidate. 2D structure was predicted by PRED-TMBB, 3D structure and functional analysis was also performed. Protein–protein interaction network of potential drug target proteins was analyzed by using STRING. The identified drug targets are expected to have great potential for designing novel drugs against VRSA infections and further screening of the compounds against these new targets may result in the discovery of novel therapeutic compounds that can be effective against Vancomycin resistant S. aureus. [Display omitted] •We identified potential drug target for VRSA strains.•We selected non-human homologue essential proteins involved in metabolic pathways.•19 proteins in unique pathways were found.•26 human nonhomologous membrane-bound proteins were identified.•pbpA penicillin-binding protein 1 and hypothetical protein MQW_01796 as the best drug target