International Journal of Computational Bioinformatics and In Silico Modeling Vol. 4, No. 1 (2015): 585-591 Research Article Open Access ISSN: 2320-0634 In silico identification of putative drug targets in methicillin resistant Staphylococcus aureus: a subtractive genomic approach Ononamadu Chimaobi James 1 *, Umeoguaju Uchenna Francis 2 , Owolarafe Tajudeen Alowonle 1 , Udedi Stanley Chukwudi 2 , Barau Muhammad Mustapha 1 and Ofoegbu Chukwudi Jude 3 1 Dept of Biochemistry and Forensic Science, Nigeria Police Academy, Wudil, Kano State, Nigeria. 2 Dept of Applied Biochemistry, NnamdiAzikiwe University, Awka, Anambra State, Nigeria. 3 Biochemisty uint of the Dept of Science Laboratory Technology, Federal University of Technology. Owerri, Imo State, Nigeria. *Corresponding author: Ononamadu Chimaobi James; e-mail: ononamaducj0016@gmail.com; Tel: +2348037202476 ABSTRACT Staphylococcus aureus is a gram positive, coagulase positive coccus in the family staphyloccocaceae. It is an opportunistic organism that has emerged as one of the predominant pathogens in community and healthcare- associated infections with limited and less effective options for treatment in the face of a rising trend in the emergence of resistant strains. This fact has necessitated the search for alternative targets for development of new drugs. In this present study, a subtractive genomic (proteome) approach was used to identify potential drug targets in methicillin resistant Staphylococcus aureus using strain 252 (MSRA252). The complete proteome of MSRA 252 obtained from Uniprot database was subjected to CD-hit suite for clustering; NCBI BlastP suite against the human proteome to exclude homologous proteins; and sequence homology with Database of Essential Genes(DEG) to determine the indispensability of the proteins for the bacteria survival. The essential proteins were further analyzed to predict the metabolic pathways they were involved in using KEGG automatic annotation server (KAAS) and their subcellular locations using, Uniprot and PsortB suite subsequently. The sequence sorting, segregation and formatting was carried out using UFS Sequence Analysis Application after each successive step. The study identified 291 essential non homologous proteins to human out of 2640. Further analysis with KAAS revealed that 114 (33 predicted membrane-associated) of the essential non homologous proteins were involved in different metabolic pathways in the organism and 60 of these were implicated in pathways unique to the bacteria relative to human (host). The study revealed a number of putative, essential non homologous protein candidates that could be further explored for the development of alternative treatments and vaccines for methicillin resistant Staphylococcus aureus infections. Keywords: Subtractive genomics, BlastP, CD-hit, KAAS, MSRA 252. 1.0 INTRODUCTION Staphylococcus aureus was first identified by Rosenbach in 1884 as a pathogen of wound infections and furunculosis. It is a common cause of skin and soft tissue infections worldwide and has also been implicated in conditions such as furuncle/carbuncles, cellulities, septic thrombophlebitis, bacteraemia, epidural abscess, osteomyelitis and prosthestic joint infection[1-2]. Staphylococcus aureus is a versatile and virulent pathogen. It has become a global health concern especially in health care setting because of the increasing high incidence, morbidity and antimicrobial resistance[3]. Approximately 20% of healthy persons are persistent carriers and 60% are intermittent carriers of S.aureus. Its resistance to methicillin dates back to 1961 soon after the introduction of the drug Received: 18 November 2014 Accepted: 16 December 2014 Online: 01 January 2015 http://bioinfo.aizeonpublishers.net/content/2015/1/bioinfo585-591.pdf 585