Literature DB >> 22300758

A metabolic network approach for the identification and prioritization of antimicrobial drug targets.

Arvind K Chavali1, Kevin M D'Auria, Erik L Hewlett, Richard D Pearson, Jason A Papin.   

Abstract

For many infectious diseases, novel treatment options are needed in order to address problems with cost, toxicity and resistance to current drugs. Systems biology tools can be used to gain valuable insight into pathogenic processes and aid in expediting drug discovery. In the past decade, constraint-based modeling of genome-scale metabolic networks has become widely used. Focusing on pathogen metabolic networks, we review in silico strategies used to identify effective drug targets and highlight recent successes as well as limitations associated with such computational analyses. We further discuss how accounting for the host environment and even targeting the host may offer new therapeutic options. These systems-level approaches are beginning to provide novel avenues for drug targeting against infectious agents.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22300758      PMCID: PMC3299924          DOI: 10.1016/j.tim.2011.12.004

Source DB:  PubMed          Journal:  Trends Microbiol        ISSN: 0966-842X            Impact factor:   17.079


  79 in total

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Authors:  Paul D Dobson; Yogendra Patel; Douglas B Kell
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Review 2.  Revisiting the host as a growth medium.

Authors:  Stacie A Brown; Kelli L Palmer; Marvin Whiteley
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Review 3.  Network pharmacology: the next paradigm in drug discovery.

Authors:  Andrew L Hopkins
Journal:  Nat Chem Biol       Date:  2008-11       Impact factor: 15.040

4.  Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001.

Authors:  Ali Navid; Eivind Almaas
Journal:  Mol Biosyst       Date:  2009-01-26

5.  Metabolic network model of a human oral pathogen.

Authors:  Varun Mazumdar; Evan S Snitkin; Salomon Amar; Daniel Segrè
Journal:  J Bacteriol       Date:  2008-10-17       Impact factor: 3.490

6.  Network-based prediction of human tissue-specific metabolism.

Authors:  Tomer Shlomi; Moran N Cabili; Markus J Herrgård; Bernhard Ø Palsson; Eytan Ruppin
Journal:  Nat Biotechnol       Date:  2008-09       Impact factor: 54.908

Review 7.  Genome-scale models of bacterial metabolism: reconstruction and applications.

Authors:  Maxime Durot; Pierre-Yves Bourguignon; Vincent Schachter
Journal:  FEMS Microbiol Rev       Date:  2008-12-03       Impact factor: 16.408

8.  targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

Authors:  Karthik Raman; Kalidas Yeturu; Nagasuma Chandra
Journal:  BMC Syst Biol       Date:  2008-12-19

9.  Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii.

Authors:  Nanette R Boyle; John A Morgan
Journal:  BMC Syst Biol       Date:  2009-01-07

10.  Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.

Authors:  Jacek Puchałka; Matthew A Oberhardt; Miguel Godinho; Agata Bielecka; Daniela Regenhardt; Kenneth N Timmis; Jason A Papin; Vítor A P Martins dos Santos
Journal:  PLoS Comput Biol       Date:  2008-10-31       Impact factor: 4.475

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  37 in total

Review 1.  ESKAPEing the labyrinth of antibacterial discovery.

Authors:  Ruben Tommasi; Dean G Brown; Grant K Walkup; John I Manchester; Alita A Miller
Journal:  Nat Rev Drug Discov       Date:  2015-07-03       Impact factor: 84.694

Review 2.  Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Authors:  Peter Csermely; Tamás Korcsmáros; Huba J M Kiss; Gábor London; Ruth Nussinov
Journal:  Pharmacol Ther       Date:  2013-02-04       Impact factor: 12.310

Review 3.  Novel antimicrobial development using genome-scale metabolic model of Gram-negative pathogens: a review.

Authors:  Wan Yean Chung; Yan Zhu; Mohd Hafidz Mahamad Maifiah; Naveen Kumar Hawala Shivashekaregowda; Eng Hwa Wong; Nusaibah Abdul Rahim
Journal:  J Antibiot (Tokyo)       Date:  2020-09-08       Impact factor: 2.649

4.  A multi-scale approach to designing therapeutics for tuberculosis.

Authors:  Jennifer J Linderman; Nicholas A Cilfone; Elsje Pienaar; Chang Gong; Denise E Kirschner
Journal:  Integr Biol (Camb)       Date:  2015-04-30       Impact factor: 2.192

5.  Linking genome-scale metabolic modeling and genome annotation.

Authors:  Edik M Blais; Arvind K Chavali; Jason A Papin
Journal:  Methods Mol Biol       Date:  2013

6.  Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis.

Authors:  Mingyuan Tian; Jennifer L Reed
Journal:  Bioinformatics       Date:  2018-11-15       Impact factor: 6.937

7.  Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism.

Authors:  Nadine Veith; Margrete Solheim; Koen W A van Grinsven; Brett G Olivier; Jennifer Levering; Ruth Grosseholz; Jeroen Hugenholtz; Helge Holo; Ingolf Nes; Bas Teusink; Ursula Kummer
Journal:  Appl Environ Microbiol       Date:  2014-12-19       Impact factor: 4.792

8.  Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions.

Authors:  Elsje Pienaar; William M Matern; Jennifer J Linderman; Joel S Bader; Denise E Kirschner
Journal:  Infect Immun       Date:  2016-04-22       Impact factor: 3.441

9.  Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.

Authors:  Sidhartha Chaudhury; Mohamed Diwan M Abdulhameed; Narender Singh; Gregory J Tawa; Patrik M D'haeseleer; Adam T Zemla; Ali Navid; Carol E Zhou; Matthew C Franklin; Jonah Cheung; Michael J Rudolph; James Love; John F Graf; David A Rozak; Jennifer L Dankmeyer; Kei Amemiya; Simon Daefler; Anders Wallqvist
Journal:  PLoS One       Date:  2013-05-21       Impact factor: 3.240

Review 10.  Computational nanomedicine: modeling of nanoparticle-mediated hyperthermal cancer therapy.

Authors:  Chanchala D Kaddi; John H Phan; May D Wang
Journal:  Nanomedicine (Lond)       Date:  2013-08       Impact factor: 5.307

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