Prioritization of potential drug targets against P. aeruginosa by core proteomic analysis using computational subtractive genomics and Protein-Protein interaction network. (June 2018)

• Record Type: Journal Article
• Authors: Uddin, Reaz; Jamil, Faiza
• Is Part Of: Computational biology and chemistry. Volume 74(2018)
• Page Start: 115
• Page End: 122
• Publication Date: 2018-06
• Subjects: P. aeruginosa -- Drug targets -- Protein-Protein interactions -- PPI -- Essentiality -- Genomics -- Drug resistance; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2018.02.017
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Highlights: Core proteomic analysis of completed proteomes of 68 strains of P. aeruginosa . Metabolic Pathways analysis of core proteomic data of P. aeruginosa . Potential drug targets prioritization against P. aeruginosa . Protein-Protein Interaction studies and hub proteins identification among hypothetical proteins of P. aeruginosa . Abstract: Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core proteomic analysis and Protein-Protein Interactions (PPIs) studies. The non-redundant reference proteome of 68 strains having complete genome and latest assembly version of P. aeruginosa were downloaded from ftp NCBI RefSeq server in October 2016. Th e standalone CD-HIT tool was used to cluster ortholog proteins (having >=80% amino acid identity) present in all strains. The pan-proteome was clustered in 12, 380 Clusters of Orthologous Proteins (COPs). By using in-house shell scripts, 3252 common COPs were extracted out and designated as clusters of core proteome. The core proteome of PAO1 strain was selected by fetching PAO1's proteome from common COPs. As a result, 1212 proteins were shortlisted that are non-homologous to the human but essential for the survival of the pathogen. Among these 1212 proteins, 321 proteins are conserved hypothetical proteins. Considering their potential as drug target, those 321 hypothetical proteins were selected and their probable functions were characterized. Based on the druggability criteria, 18 proteins were shortlisted. The interacting partners were identified by investigating the PPIs network using STRING v10 database. Subsequently, 8 proteins were shortlisted as 'hub proteins' and proposed as potential novel drug targets against P. aeruginosa . The study is interesting for the scientific community working to identify novel drug targets against MDR pathogens particularly P. aeruginosa .