In silico subtractive genomics for target identification in human bacterial pathogens

Abstract

Target identification is the first step in the drug and vaccine discovery process; in silico subtractive genomics is widely used in this process. Using this approach, in recent years, a large number of targets have been identified for bacterial pathogens that are either drug resistant or for which no suitable vaccine is available; most such reports concern a specific pathogen. The in silico method reduces the time as well as the cost of target screening. Although a powerful technique that can be applied to a wide range of pathogens, there are many pitfalls in the analysis and interpretation of the data. We review this approach, including targets that have been identified with this technique and various other aspects, including advantages and disadvantages. We also discuss our own experiences using this technology. Drug Dev Res 72: 162-177, 2011.

A comprehensive computational mutation structurefunction approach for determining potential drug target sites in poliovirus 2A protease

“…Cytoplasmic proteins tend to have more potential as drug targets compared to surface membrane proteins [34]. The CELLO v.2.5 [35] server was employed to predict subcellular localization of poliovirus 2A protease.…”

Phytocomponent 4-hydroxy-3-methoxycinnamaldehyde ablates T-cell activation by targeting protein kinase C-θ and its downstream pathways

“…Nevertheless, computational tools significantly accelerate the process of target validation, increase treatment possibilities and decrease the rate of drug failure in the final phase of clinical trials. Computational tools well-thought-out with 'omics' data (proteomics, genomics and metabolomics) are attractive tools for searching of likely targets and off-targets for potent small molecules [14][15][16]. In silico studies enabled us not only to identify the target proteins of 4H3MC but also to unravel its suppressive mechanism in T cells.…”

Computational Identification of Putative Drug Targets in Malassezia Globosa by Subtractive Genomics and Protein Cluster Network Approach

“…Identification of putative drug targets from annotated metabolic pathways available in KEGG using subtractive genomics/ proteomics has been widely used by several researchers in bacterial pathogens [33][34][35][36][37][38]. Metabolic pathways that are present in both the host and the pathogen are identified as common pathways and those which are present only in infection causing organism but not in the host as unique pathways.…”