Literature DB >> 21552346

In Silico Augmentation of the Drug Development Pipeline: Examples from the study of Acute Inflammation.

Gary An1, John Bartels, Yoram Vodovotz.   

Abstract

The clinical translation of promising basic biomedical findings, whether derived from reductionist studies in academic laboratories or as the product of extensive high-throughput and -content screens in the biotechnology and pharmaceutical industries, has reached a period of stagnation in which ever higher research and development costs are yielding ever fewer new drugs. Systems biology and computational modeling have been touted as potential avenues by which to break through this logjam. However, few mechanistic computational approaches are utilized in a manner that is fully cognizant of the inherent clinical realities in which the drugs developed through this ostensibly rational process will be ultimately used. In this article, we present a Translational Systems Biology approach to inflammation. This approach is based on the use of mechanistic computational modeling centered on inherent clinical applicability, namely that a unified suite of models can be applied to generate in silico clinical trials, individualized computational models as tools for personalized medicine, and rational drug and device design based on disease mechanism.

Entities:  

Year:  2011        PMID: 21552346      PMCID: PMC3086282          DOI: 10.1002/ddr.20415

Source DB:  PubMed          Journal:  Drug Dev Res        ISSN: 0272-4391            Impact factor:   4.360


  109 in total

Review 1.  Metabolic networks: a signal-oriented approach to cellular models.

Authors:  J W Lengeler
Journal:  Biol Chem       Date:  2000 Sep-Oct       Impact factor: 3.915

2.  The role of initial trauma in the host's response to injury and hemorrhage: insights from a correlation of mathematical simulations and hepatic transcriptomic analysis.

Authors:  Claudio E Lagoa; John Bartels; Arie Baratt; George Tseng; Gilles Clermont; Mitchell P Fink; Timothy R Billiar; Yoram Vodovotz
Journal:  Shock       Date:  2006-12       Impact factor: 3.454

Review 3.  Using computational modeling to drive the development of targeted therapeutics.

Authors:  Ulrik B Nielsen; Brigit Schoeberl
Journal:  IDrugs       Date:  2005-10

4.  In silico experiments of existing and hypothetical cytokine-directed clinical trials using agent-based modeling.

Authors:  Gary An
Journal:  Crit Care Med       Date:  2004-10       Impact factor: 7.598

5.  A reduced mathematical model of the acute inflammatory response II. Capturing scenarios of repeated endotoxin administration.

Authors:  Judy Day; Jonathan Rubin; Yoram Vodovotz; Carson C Chow; Angela Reynolds; Gilles Clermont
Journal:  J Theor Biol       Date:  2006-04-17       Impact factor: 2.691

6.  A reduced mathematical model of the acute inflammatory response: I. Derivation of model and analysis of anti-inflammation.

Authors:  Angela Reynolds; Jonathan Rubin; Gilles Clermont; Judy Day; Yoram Vodovotz; G Bard Ermentrout
Journal:  J Theor Biol       Date:  2006-04-03       Impact factor: 2.691

7.  A mathematical simulation of the inflammatory response to anthrax infection.

Authors:  Rukmini Kumar; Carson C Chow; John D Bartels; Gilles Clermont; Yoram Vodovotz
Journal:  Shock       Date:  2008-01       Impact factor: 3.454

Review 8.  The yin and yang of tumor necrosis factor inhibitors.

Authors:  Leonard Calabrese
Journal:  Cleve Clin J Med       Date:  2006-03       Impact factor: 2.321

9.  SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.

Authors:  Alexey Solovyev; Maxim Mikheev; Leming Zhou; Joyeeta Dutta-Moscato; Cordelia Ziraldo; Gary An; Yoram Vodovotz; Qi Mi
Journal:  Int J Agent Technol Syst       Date:  2010

Review 10.  Docking, virtual high throughput screening and in silico fragment-based drug design.

Authors:  Vincent Zoete; Aurélien Grosdidier; Olivier Michielin
Journal:  J Cell Mol Med       Date:  2009-01-21       Impact factor: 5.310

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  20 in total

Review 1.  From data patterns to mechanistic models in acute critical illness.

Authors:  Jean-Marie Aerts; Wassim M Haddad; Gary An; Yoram Vodovotz
Journal:  J Crit Care       Date:  2014-03-29       Impact factor: 3.425

2.  A two-compartment mathematical model of endotoxin-induced inflammatory and physiologic alterations in swine.

Authors:  Gary Nieman; David Brown; Joydeep Sarkar; Brian Kubiak; Cordelia Ziraldo; Joyeeta Dutta-Moscato; Christopher Vieau; Derek Barclay; Louis Gatto; Kristopher Maier; Gregory Constantine; Timothy R Billiar; Ruben Zamora; Qi Mi; Steve Chang; Yoram Vodovotz
Journal:  Crit Care Med       Date:  2012-04       Impact factor: 7.598

3.  Inflammation and Disease: Modelling and Modulation of the Inflammatory Response to Alleviate Critical Illness.

Authors:  Judy D Day; Chase Cockrell; Rami Namas; Ruben Zamora; Gary An; Yoram Vodovotz
Journal:  Curr Opin Syst Biol       Date:  2018-08-23

4.  Computational Modeling of Inflammation and Wound Healing.

Authors:  Cordelia Ziraldo; Qi Mi; Gary An; Yoram Vodovotz
Journal:  Adv Wound Care (New Rochelle)       Date:  2013-11       Impact factor: 4.730

Review 5.  Sepsis: from pattern to mechanism and back.

Authors:  Gary An; Rami A Namas; Yoram Vodovotz
Journal:  Crit Rev Biomed Eng       Date:  2012

6.  Sepsis: Something old, something new, and a systems view.

Authors:  Rami Namas; Ruben Zamora; Rajaie Namas; Gary An; John Doyle; Thomas E Dick; Frank J Jacono; Ioannis P Androulakis; Gary F Nieman; Steve Chang; Timothy R Billiar; John A Kellum; Derek C Angus; Yoram Vodovotz
Journal:  J Crit Care       Date:  2011-07-27       Impact factor: 3.425

Review 7.  The inverse problem in mathematical biology.

Authors:  Gilles Clermont; Sven Zenker
Journal:  Math Biosci       Date:  2014-10-18       Impact factor: 2.144

Review 8.  In silico modeling: methods and applications to trauma and sepsis.

Authors:  Yoram Vodovotz; Timothy R Billiar
Journal:  Crit Care Med       Date:  2013-08       Impact factor: 7.598

9.  Computational and systems biology in trauma and sepsis: current state and future perspectives.

Authors:  Gary An; Gary Nieman; Yoram Vodovotz
Journal:  Int J Burns Trauma       Date:  2012-02-01

Review 10.  Multiscale Modeling in the Clinic: Drug Design and Development.

Authors:  Colleen E Clancy; Gary An; William R Cannon; Yaling Liu; Elebeoba E May; Peter Ortoleva; Aleksander S Popel; James P Sluka; Jing Su; Paolo Vicini; Xiaobo Zhou; David M Eckmann
Journal:  Ann Biomed Eng       Date:  2016-02-17       Impact factor: 3.934

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