Research paper Identification of putative drug targets in Vancomycin-resistant Staphylococcus aureus (VRSA) using computer aided protein data analysis Md. Anayet Hasan a, ⁎, Md. Arif Khan b , Tahmina Sharmin b , Md. Habibul Hasan Mazumder a , Afrin Sultana Chowdhury a a Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh b Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh abstract article info Article history: Received 16 February 2015 Received in revised form 20 August 2015 Accepted 23 August 2015 Available online 28 August 2015 Keywords: VRSA Genome subtraction Metabolic pathway Drug target Network analysis 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. © 2015 Elsevier B.V. All rights reserved. 1. Introduction Staphylococcus aureus is a Gram-positive spherical bacterium that is a member of Staphylococcacea family. Among more than 20 species of Staphylococcus described in Bergey's Manual (2001), it is the most significant because of its interactions both with humans and different livestock (Lowy, 1998). Serious infections caused by S. aureus are a worldwide phenomenon and occur in both the hospital and community settings (Emmerson, 1994; Locksley et al., 1982). It is responsible for causing a variety of suppurative (pus-forming) infections of skin and toxinoses in humans (Carleton et al., 2004; King et al., 2006). It is also related with hospital acquired (nosocomial) infection of surgical wounds (Wisplinghoff et al., 2004), osteomyelitis, ostitis, bacteraemia (Shaposhnikova et al., 1995) and infections associated with in dwelling medical devices (Kuroda et al., 2001; Richards et al., 1999). S. aureus causes food poisoning by producing enterotoxins into food, and is related with toxic shock syndrome by releasing super-antigens into blood (Chong et al., 2006; Diekema et al., 2011). Studies have also shown its involvement in infecting patients with diabetes, cardiovascular and other chronic diseases (Tuo et al., 1995). Besides these it is also found in human skin and causes some major problems like sour throat, pimple, acne, hair follicle infection, and sties (inflammation of an eyelid gland). Its pathogenicity includes numerous enzymes like coagulase Gene 575 (2016) 132–143 Abbreviations: MRSA, Methicillin-resistant Staphylococcus aureus; VISA, Vancomycin- intermediate-resistant Staphylococcus aureus; VRSA, Vancomycin-resistant Staphylococcus aureus; CD-HIT, Cluster Database at High Identity with Tolerance; BLAST, Basic Local Alignment Search Tool; E-value, expectation value; MSP, maximal segment pair; DEG, database of essential gene; KEGG, Kyoto Encyclopedia of Genes and Genomes; KAAS, KEGG Automatic Annotation Server; SVM, Support Vector Machine; DB, Drug Bank; FDA, Food and Drug Administration; OMP, outer membrane proteins; PPI, protein–protein interaction; STRING, Search Tool for the Retrieval of Interacting Genes/Proteins; PTS, phosphotransferase system; PEP, phosphoenolpyruvate; ddl, D-alanyl-alanine synthetase A; 3D, three dimensional. ⁎ Corresponding author. E-mail address: anayet_johny@yahoo.com (M.A. Hasan). http://dx.doi.org/10.1016/j.gene.2015.08.044 0378-1119/© 2015 Elsevier B.V. All rights reserved. Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene