title: A formal model for analyzing drug combination effects and its application in TNF-alpha-induced NFkappaB pathway.
abstract: BACKGROUND
  Drug combination therapy is commonly used in clinical practice. Many methods including Bliss independence method have been proposed for drug combination design based on simulations models or experiments. Although Bliss independence method can help to solve the drug combination design problem when there are only a small number of combinations, as the number of combinations increases, it may not be scalable. Exploration of system structure becomes important to reduce the complexity of the design problem.
  
  
  RESULTS
  In this paper, we deduced a mathematical model which can simplify the serial structure and parallel structure of biological pathway for synergy evaluation of drug combinations. We demonstrated in steady state the sign of the synergism assessment factor derivative of the original system can be predicted by the sign of its simplified system. In addition, we analyzed the influence of feedback structure on survival ratio of the serial structure. We provided a sufficient condition under which the combination effect could be maintained. Furthermore, we applied our method to find three synergistic drug combinations on tumor necrosis factor alpha-induced NFkappaB pathway and subsequently verified by the cell experiment.
  
  
  CONCLUSIONS
  We identified several structural properties underlying the Bliss independence criterion, and developed a systematic simplification framework for drug combination design by combining simulation and system reaction network topology analysis. We hope that this work can provide insights to tackle the challenging problem of assessment of combinational drug therapy effect in a large scale signaling pathway. And hopefully in the future our method could be expanded to more general criteria.
authors.affiliation: Department of Automation and TNList, Tsinghua University, Beijing, 100084, China.
authors.forename: Han
authors.initials: H
authors.lastname: Yan
authors.forename: Bo
authors.initials: B
authors.lastname: Zhang
authors.forename: Shao
authors.initials: S
authors.lastname: Li
authors.forename: Qianchuan
authors.initials: Q
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D002478:Cells, Cultured / Q000187:drug effects; D002626:Chemistry, Pharmaceutical / Q000379:methods*; D004338:Drug Combinations; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D004358:Drug Therapy / Q000379:methods; D004730:Endothelium, Vascular / Q000187:drug effects; D006801:Humans; D008954:Models, Biological; D015233:Models, Statistical; D008962:Models, Theoretical; D016328:NF-kappa B / Q000378:metabolism*; D049490:Systems Biology; D016896:Treatment Outcome; D014409:Tumor Necrosis Factor-alpha / Q000378:metabolism*
chemical_list: D004338:Drug Combinations; D016328:NF-kappa B; D014409:Tumor Necrosis Factor-alpha