Literature DB >> 22999913

Mechanistic systems modeling to guide drug discovery and development.

Brian J Schmidt1, Jason A Papin, Cynthia J Musante.   

Abstract

A crucial question that must be addressed in the drug development process is whether the proposed therapeutic target will yield the desired effect in the clinical population. Pharmaceutical and biotechnology companies place a large investment on research and development, long before confirmatory data are available from human trials. Basic science has greatly expanded the computable knowledge of disease processes, both through the generation of large omics data sets and a compendium of studies assessing cellular and systemic responses to physiologic and pathophysiologic stimuli. Given inherent uncertainties in drug development, mechanistic systems models can better inform target selection and the decision process for advancing compounds through preclinical and clinical research.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22999913      PMCID: PMC3644584          DOI: 10.1016/j.drudis.2012.09.003

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  107 in total

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2.  The failure of torcetrapib: was it the molecule or the mechanism?

Authors:  Alan R Tall; Laurent Yvan-Charvet; Nan Wang
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3.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

Authors:  Jan Schellenberger; Richard Que; Ronan M T Fleming; Ines Thiele; Jeffrey D Orth; Adam M Feist; Daniel C Zielinski; Aarash Bordbar; Nathan E Lewis; Sorena Rahmanian; Joseph Kang; Daniel R Hyduke; Bernhard Ø Palsson
Journal:  Nat Protoc       Date:  2011-08-04       Impact factor: 13.491

Review 4.  The productivity crisis in pharmaceutical R&D.

Authors:  Fabio Pammolli; Laura Magazzini; Massimo Riccaboni
Journal:  Nat Rev Drug Discov       Date:  2011-06       Impact factor: 84.694

5.  The Type 1 Diabetes PhysioLab Platform: a validated physiologically based mathematical model of pathogenesis in the non-obese diabetic mouse.

Authors:  L Shoda; H Kreuwel; K Gadkar; Y Zheng; C Whiting; M Atkinson; J Bluestone; D Mathis; D Young; S Ramanujan
Journal:  Clin Exp Immunol       Date:  2010-05-18       Impact factor: 4.330

6.  Drug off-target effects predicted using structural analysis in the context of a metabolic network model.

Authors:  Roger L Chang; Li Xie; Lei Xie; Philip E Bourne; Bernhard Ø Palsson
Journal:  PLoS Comput Biol       Date:  2010-09-23       Impact factor: 4.475

7.  A genome-scale, constraint-based approach to systems biology of human metabolism.

Authors:  Monica L Mo; Neema Jamshidi; Bernhard Ø Palsson
Journal:  Mol Biosyst       Date:  2007-07-11

8.  Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease.

Authors:  Arvind K Chavali; Anna S Blazier; Jose L Tlaxca; Paul A Jensen; Richard D Pearson; Jason A Papin
Journal:  BMC Syst Biol       Date:  2012-04-27

9.  Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.

Authors:  Anu Raghunathan; Jennifer Reed; Sookil Shin; Bernhard Palsson; Simon Daefler
Journal:  BMC Syst Biol       Date:  2009-04-08

10.  The Edinburgh human metabolic network reconstruction and its functional analysis.

Authors:  Hongwu Ma; Anatoly Sorokin; Alexander Mazein; Alex Selkov; Evgeni Selkov; Oleg Demin; Igor Goryanin
Journal:  Mol Syst Biol       Date:  2007-09-18       Impact factor: 11.429

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  20 in total

1.  GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.

Authors:  Brian J Schmidt; Ali Ebrahim; Thomas O Metz; Joshua N Adkins; Bernhard Ø Palsson; Daniel R Hyduke
Journal:  Bioinformatics       Date:  2013-08-23       Impact factor: 6.937

2.  QSP Toolbox: Computational Implementation of Integrated Workflow Components for Deploying Multi-Scale Mechanistic Models.

Authors:  Yougan Cheng; Craig J Thalhauser; Shepard Smithline; Jyotsna Pagidala; Marko Miladinov; Heather E Vezina; Manish Gupta; Tarek A Leil; Brian J Schmidt
Journal:  AAPS J       Date:  2017-05-24       Impact factor: 4.009

Review 3.  In silico methods for drug repurposing and pharmacology.

Authors:  Rachel A Hodos; Brian A Kidd; Khader Shameer; Ben P Readhead; Joel T Dudley
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2016-04-15

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.  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

6.  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 7.  Artificial Intelligence and the Future of Diagnostic and Therapeutic Radiopharmaceutical Development:: In Silico Smart Molecular Design.

Authors:  Bahar Ataeinia; Pedram Heidari
Journal:  PET Clin       Date:  2021-08-05

Review 8.  Enhancing the discovery and development of immunotherapies for cancer using quantitative and systems pharmacology: Interleukin-12 as a case study.

Authors:  David J Klinke
Journal:  J Immunother Cancer       Date:  2015-06-16       Impact factor: 13.751

9.  Alternate virtual populations elucidate the type I interferon signature predictive of the response to rituximab in rheumatoid arthritis.

Authors:  Brian J Schmidt; Fergal P Casey; Thomas Paterson; Jason R Chan
Journal:  BMC Bioinformatics       Date:  2013-07-10       Impact factor: 3.169

Review 10.  Bridging Systems Medicine and Patient Needs.

Authors:  J-P Boissel; C Auffray; D Noble; L Hood; F-H Boissel
Journal:  CPT Pharmacometrics Syst Pharmacol       Date:  2015-03-27
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