Literature DB >> 21704158

Emergence of the silicon human and network targeting drugs.

Alexey Kolodkin1, Fred C Boogerd, Nick Plant, Frank J Bruggeman, Valeri Goncharuk, Jeantine Lunshof, Rafael Moreno-Sanchez, Nilgun Yilmaz, Barbara M Bakker, Jacky L Snoep, Rudi Balling, Hans V Westerhoff.   

Abstract

The development of disease may be characterized as a pathological shift of homeostasis; the main goal of contemporary drug treatment is, therefore, to return the pathological homeostasis back to the normal physiological range. From the view point of systems biology, homeostasis emerges from the interactions within the network of biomolecules (e.g. DNA, mRNA, proteins), and, hence, understanding how drugs impact upon the entire network should improve their efficacy at returning the network (body) to physiological homeostasis. Large, mechanism-based computer models, such as the anticipated human whole body models (silicon or virtual human), may help in the development of such network-targeting drugs. Using the philosophical concept of weak and strong emergence, we shall here take a more general look at the paradigm of network-targeting drugs, and propose our approaches to scale the strength of strong emergence. We apply these approaches to several biological examples and demonstrate their utility to reveal principles of bio-modeling. We discuss this in the perspective of building the silicon human. Crown
Copyright © 2011. Published by Elsevier B.V. All rights reserved.

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Year:  2011        PMID: 21704158     DOI: 10.1016/j.ejps.2011.06.006

Source DB:  PubMed          Journal:  Eur J Pharm Sci        ISSN: 0928-0987            Impact factor:   4.384


  12 in total

Review 1.  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 2.  From gene networks to drugs: systems pharmacology approaches for AUD.

Authors:  Laura B Ferguson; R Adron Harris; Roy Dayne Mayfield
Journal:  Psychopharmacology (Berl)       Date:  2018-03-01       Impact factor: 4.530

Review 3.  Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease.

Authors:  Ciarán P Fisher; Andrzej M Kierzek; Nick J Plant; J Bernadette Moore
Journal:  World J Gastroenterol       Date:  2014-11-07       Impact factor: 5.742

4.  A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics.

Authors:  Pramod Rajaram Somvanshi; K V Venkatesh
Journal:  Syst Synth Biol       Date:  2013-09-18

5.  Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence.

Authors:  Alexey Kolodkin; Evangelos Simeonidis; Rudi Balling; Hans V Westerhoff
Journal:  Front Physiol       Date:  2012-07-23       Impact factor: 4.566

Review 6.  Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery.

Authors:  Douglas B Kell; Royston Goodacre
Journal:  Drug Discov Today       Date:  2013-07-26       Impact factor: 7.851

7.  QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells.

Authors:  Ciarán P Fisher; Nicholas J Plant; J Bernadette Moore; Andrzej M Kierzek
Journal:  Bioinformatics       Date:  2013-09-23       Impact factor: 6.937

8.  Macromolecular networks and intelligence in microorganisms.

Authors:  Hans V Westerhoff; Aaron N Brooks; Evangelos Simeonidis; Rodolfo García-Contreras; Fei He; Fred C Boogerd; Victoria J Jackson; Valeri Goncharuk; Alexey Kolodkin
Journal:  Front Microbiol       Date:  2014-07-22       Impact factor: 5.640

9.  Systems medicine of inflammaging.

Authors:  Gastone C Castellani; Giulia Menichetti; Paolo Garagnani; Maria Giulia Bacalini; Chiara Pirazzini; Claudio Franceschi; Sebastiano Collino; Claudia Sala; Daniel Remondini; Enrico Giampieri; Ettore Mosca; Matteo Bersanelli; Silvia Vitali; Italo Faria do Valle; Pietro Liò; Luciano Milanesi
Journal:  Brief Bioinform       Date:  2015-08-24       Impact factor: 11.622

10.  Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology.

Authors:  Joanna H Sier; Alfred E Thumser; Nick J Plant
Journal:  BMC Syst Biol       Date:  2017-12-15
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