Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study

2012 ◽  
Vol 57 ◽  
pp. 185-195 ◽  
Author(s):  
Aditya Sharma ◽  
Archana Pan
Keyword(s):  
Yersinia Pestis ◽  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Drug Targets ◽  
Potential Drug ◽  
Metabolic Pathway Analysis ◽  
Potential Drug Targets

scholarly journals Deciphering Potential Drug Targets in Clostridium Perfringens through Metabolic Pathway Analysis

2019 ◽  
pp. 432-437
Author(s):  
M Arockiyajainmary ◽  
Sivashankari Selvarajan
Keyword(s):  
Clostridium Perfringens ◽  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Metabolic Pathways ◽  
Drug Targets ◽  
Cellular Localization ◽  
Potential Drug ◽  
Metabolic Pathway Analysis ◽  
Homologous Proteins ◽  
Potential Drug Targets

Background: In our day-to-day life, we are facing many dreadful diseases caused by many infectious pathogens. These pathogens invade the living organisms (host) and lethally damaging them. These dreadful pathogens were also be used as bioweapons. Among them, Clostridium perfringens is taken for the study. Clostridium perfringens is an anaerobic, rod shaped, gram positive bacteria capable of forming spores. It is prevalent in the environment and in the intestine of humans and other animals. It is the causative agent for a wide range of diseases including food borne diseases, gas gangrene and flesh eating disease called necrotizing fasciitis. C. perfringens is commonly found on raw meat and poultry that espouse to grow in conditions with very little or no oxygen, and under ideal conditions can multiply very rapidly. These conditions are occasionally lethal due to the substantial number of toxins such as alpha toxin, beta toxin, epsilon toxin and iota toxin produced by C. perfringens. It is significantly important to analyze the Drug targets of the pathogen in order to destroy them. Objective: The present work aims in identifying potential drug targets in C. perfringens through metabolic pathway analysis. Method: Primarily, the metabolic pathways of the host and pathogen are compared to identify unique pathways in the bacteria. Among the enzymes that catalyze unique metabolic pathways, the essential ones for the survival of the pathogen are identified. The druggability of the essential enzymes are predicted through identification of its sub cellular localization and other druggable parameters. Results: The comparative metabolic pathway analysis result shows that, among the 98 metabolic pathways of C.perfringens, 25 pathways were unique that they did not have a counterpart with Human. There were 113 enzymes involved in these unique pathways. The NCBI’s protein Blast search against human was done to identify the non-homologous proteins. There were 93 non-homologous proteins. Among the 93 non-homologous proteins, 47 proteins were found to be essential. Based on their sub-cellular localization, 32 proteins were identified as potential drug targets and 15 are probable vaccine candidates. Conclusion: The present work which started with 25 different pathways with more than a hundred different enzymes, resulted in the identification of 32 putative drug targets against C.perfringens infection. All these 32 identified targets did not have any human homolog and are highly essential for the survival of the organism. They were concluded as potential drug targets. Designing of compounds to inhibit these enzymes would be successful for treating the life threatening infections caused by this pathogen.

scholarly journals “In Silico Metabolic Pathway Analysis and Docking Analysis of Treponema Pallidum Subs. Pallidum Nichols for Potential Drug Targets”

2017 ◽  
Vol 10 (5) ◽  
pp. 261
Author(s):  
Radha Mahendran
Keyword(s):  
Homology Modeling ◽  
Metabolic Pathway ◽  
Drug Targets ◽  
Active Sites ◽  
Homo Sapiens ◽  
Treponema Pallidum ◽  
Potential Drug ◽  
Metabolic Pathway Analysis ◽  
Docking Analysis ◽  
Potential Drug Targets

ABSTRACT Objective: Syphilis is a sexually transmitted infection caused by the spirochaete, Treponema pallidum subspecies pallidum nichols. In this study, a comparative metabolic pathway analysis and molecular docking was performed to identify putative drug targets.Methods: The biochemical pathways of Treponema pallidum subs. pallidum nichols and Homo sapiens were compared using KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway. The amino acid sequence of the selected enzymes were retrieved and Blastp was performed. Out of 9 enzymes, enolase was modeled using ModWeb and the structure was validated using RAMPAGE. The active sites were identified using Metapocket 2.0 and further docked using AutoDock 4.2.Results: The enzymes which were not similar to that of Homo sapiens were filtered out as potential drug targets. A total of 9 enzymes were retrieved which were present only in the Treponema pallidum subs. pallidum nichols. The structure obtained from Homology modeling was validated and further active sites were predicted. The docking analysis results showed the interaction between enolase and doxycycline and the structures were obtained using PyMol.Conclusion: Through this study, doxycycline which has antibacterial effect and a derivative of tetracycline could be one of the potential ligands. Keywords: Syphilis, Treponema pallidum, KEGG, Blastp, metabolic pathway, Homology Modeling, DockingREVIEWERSProf.G.SHOBA,Bioinformatics Department      Dr.M.G.R Janaki College of Arts and Science for Women      University of Madras      [email protected]      Phone: 9094009791 2. Prof .VINOTH,Biotechnology & Bioinformatics DepartmentHindustan University,Kelambakkam, Chennai-603103                  [email protected]                 Phone - + 91 97895 95766

scholarly journals A new approach for potential drug target discovery through in silico metabolic pathway analysis using Trypanosoma cruzi genome information

2009 ◽  
Vol 104 (8) ◽  
pp. 1100-1110 ◽  
Author(s):  
Marcelo Alves-Ferreira ◽  
Ana Carolina Ramos Guimarães ◽  
Priscila Vanessa da Silva Zabala Capriles ◽  
Laurent E Dardenne ◽  
Wim M Degrave
Keyword(s):  
Pathway Analysis ◽  
Metabolic Pathway ◽  
In Silico ◽  
Drug Target ◽  
Potential Drug Target ◽  
Potential Drug ◽  
Metabolic Pathway Analysis ◽  
Drug Target Discovery ◽  
New Approach ◽  
Genome Information

scholarly journals Metabolic pathway analysis and molecular docking analysis for identification of putative drug targets in Toxoplasma gondii: novel approach

2012 ◽  
Vol 8 (3) ◽  
pp. 134-141 ◽  
Author(s):  
Budhayash Gautam ◽  
Gurmit Singh ◽  
Gulshan Wadhwa ◽  
Rohit Farmer ◽  
Satendra Singh ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Toxoplasma Gondii ◽  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Drug Targets ◽  
Metabolic Pathway Analysis ◽  
Docking Analysis ◽  
Novel Approach ◽  
Molecular Docking Analysis

METABOLIC PATHWAY ANALYSIS OFS. PNEUMONIAE: ANIN SILICOAPPROACH TOWARDS DRUG-DESIGN

2007 ◽  
Vol 05 (01) ◽  
pp. 135-153 ◽  
Author(s):  
SHAILZA SINGH ◽  
B. K. MALIK ◽  
D. K. SHARMA
Keyword(s):  
Drug Design ◽  
Metabolic Pathway ◽  
Metabolic Pathways ◽  
Drug Targets ◽  
Nucleotide Metabolism ◽  
Rational Drug Design ◽  
Systematic Evaluation ◽  
Potential Drug ◽  
Genome Database ◽  
Potential Drug Targets

The emergence of multidrug resistant varieties of Streptococcus pneumoniae (S. pneumoniae) has led to a search for novel drug targets. An in silico comparative analysis of metabolic pathways of the host Homo sapiens (H. sapiens) and the pathogen S. pneumoniae have been performed. Enzymes from the biochemical pathways of S. pneumoniae from the KEGG metabolic pathway database were compared with proteins from the host H. sapiens, by performing a BLASTp search against the non-redundant database restricted to the H. sapiens subset. The e-value threshold cutoff was set to 0.005. Enzymes, which do not show similarity to any of the host proteins, below this threshold, were filtered out as potential drug targets. Five pathways unique to the pathogen S. pneumoniae when compared to the host H. sapiens have been identified. Potential drug targets from these pathways could be useful for the discovery of broad-spectrum drugs. Potential drug targets were also identified from pathways related to lipid metabolism, carbohydrate metabolism, amino acid metabolism, energy metabolism, vitamin and cofactor biosynthetic pathways and nucleotide metabolism. Of the 161 distinct targets identified from these pathways, many are in various stages of progress at the Microbial Genome Database. However, 44 of the targets are new and can be considered for rational drug design. The study was successful in listing out potential drug targets from the S. pneumoniae proteome involved in vital aspects of the pathogen's metabolism, persistence, virulence and cell wall biosynthesis. This systematic evaluation of metabolic pathways of host and pathogen through reliable and conventional bioinformatics approach can be extended to other pathogens of clinical interest.

Sign in / Sign up

Export Citation Format

Share Document