Yang2007_ArachidonicAcidView the 2008-08 Model of the Month entry for this model
This model is according to the paper Dynamic Simulation on the Arachidonic Acid Metabolic Network . Figure 2A has been reproduced by SBML ode solver on line. In the original model, all the reactions are presented as ODE directly. So curator rewrite each reaction according to the semantics of the paper. In this paper, the authors used quict complex kinetics law to describe the catalysis in the network, curators did not necessarily know all the complete meanings of the paper.
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
- Dynamic simulations on the arachidonic acid metabolic network.
- Yang K, Ma W, Liang H, Ouyang Q, Tang C, Lai L
- PLoS computational biology , 3/ 2007 , Volume 3 , pages: e55 , PubMed ID: 17381237
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Drug molecules not only interact with specific targets, but also alter the state and function of the associated biological network. How to design drugs and evaluate their functions at the systems level becomes a key issue in highly efficient and low-side-effect drug design. The arachidonic acid metabolic network is the network that produces inflammatory mediators, in which several enzymes, including cyclooxygenase-2 (COX-2), have been used as targets for anti-inflammatory drugs. However, neither the century-old nonsteriodal anti-inflammatory drugs nor the recently revocatory Vioxx have provided completely successful anti-inflammatory treatment. To gain more insights into the anti-inflammatory drug design, the authors have studied the dynamic properties of arachidonic acid (AA) metabolic network in human polymorphous leukocytes. Metabolic flux, exogenous AA effects, and drug efficacy have been analyzed using ordinary differential equations. The flux balance in the AA network was found to be important for efficient and safe drug design. When only the 5-lipoxygenase (5-LOX) inhibitor was used, the flux of the COX-2 pathway was increased significantly, showing that a single functional inhibitor cannot effectively control the production of inflammatory mediators. When both COX-2 and 5-LOX were blocked, the production of inflammatory mediators could be completely shut off. The authors have also investigated the differences between a dual-functional COX-2 and 5-LOX inhibitor and a mixture of these two types of inhibitors. Their work provides an example for the integration of systems biology and drug discovery.
|BIOMD0000000106_url.xml||SBML L2V1 representation of Yang2007_ArachidonicAcid||72.26 KB||Preview | Download|
|BIOMD0000000106-biopax2.owl||Auto-generated BioPAX (Level 2)||48.78 KB||Preview | Download|
|BIOMD0000000106.sci||Auto-generated Scilab file||8.85 KB||Preview | Download|
|BIOMD0000000106.pdf||Auto-generated PDF file||270.69 KB||Preview | Download|
|BIOMD0000000106.vcml||Auto-generated VCML file||83.67 KB||Preview | Download|
|BIOMD0000000106-biopax3.owl||Auto-generated BioPAX (Level 3)||68.13 KB||Preview | Download|
|BIOMD0000000106.png||Auto-generated Reaction graph (PNG)||445.32 KB||Preview | Download|
|BIOMD0000000106.m||Auto-generated Octave file||13.55 KB||Preview | Download|
|BIOMD0000000106.xpp||Auto-generated XPP file||9.69 KB||Preview | Download|
|BIOMD0000000106.svg||Auto-generated Reaction graph (SVG)||80.45 KB||Preview | Download|
|BIOMD0000000106_urn.xml||Auto-generated SBML file with URNs||76.51 KB||Preview | Download|
- Model originally submitted by : Kun Yang
- Submitted: Apr 9, 2007 8:28:33 PM
- Last Modified: Oct 10, 2014 12:07:42 PM
- Submitted on: Oct 10, 2014 12:07:42 PM
- Submitted by: Kun Yang
- With comment: Current version of Yang2007_ArachidonicAcid
- Submitted on: Apr 9, 2007 8:28:33 PM
- Submitted by: Kun Yang
- With comment: Original import of AAnetwork
(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
arachidonic acid ; Arachidonate
Leukotriene A-4 hydrolase
15(S)-HETE ; (15S)-15-Hydroxy-5,8,11-cis-13-trans-eicosatetraenoate
prostaglandin H2 ; Prostaglandin H2
thromboxane A2 ; Thromboxane A2
thromboxane B2 ; Thromboxane B2
5(S)-HPETE ; 5(S)-HPETE
5(S)-HETE ; 5(S)-HETE
|=> x1; x11, x13, x15, x2, x4||cell*K15*x15*lin*(1+x4/KI19+x2/KI20+x13/KI21+x11/KI22)/(lin+k15*(1+x1/ks))||K15 = 3600.0; KI21 = 500.0; lin = 12.0; ks = 500.0; k15 = 2600.0; KI22 = 500.0; KI19 = 500.0; KI20 = 200.0|
|x1 => x2; x16||cell*K16*x16*x1/(x1+k16*(1+x2/ks))||K16 = 1000.0; ks = 500.0; k16 = 70.0|
|x1 => x4; x17, x3||cell*K17*x17*x1/(x1+k17*(1+x4/ki18+x3/ki16+x4/ks))||ks = 500.0; ki18 = 10.0; ki16 = 10.0; k17 = 50.0; K17 = 1000.0|
|x1 => x6; x18, x7||cell*K18*x18*x1/(x1+k18*(1+x7/ki3+x6/ks))||ks = 500.0; ki3 = 30.0; K18 = 1000.0; k18 = 50.0|
|x1 => x10; x11, x3, x5, x7, x21||cell*K21*x21*x1/(x1+k21*(1+x5/ki7+x3/ki8+x7/ki11+x11/ki12+x10/ks))||k21 = 5.0; ks = 500.0; ki8 = 4.0; ki7 = 30.0; ki11 = 15.0; K21 = 5000.0; ki12 = 6.3|
|x22 => ; x12||cell*K22*x22*x12/((x12+k22)*129)||K22 = 125.0; k22 = 20.0|
|x2 => x3; x24||cell*K24*x24*x2/(x2+k24*(1+x3/ks))||ks = 500.0; k24 = 70.0; K24 = 500.0|
|x6 => x7; x1, x19, x3||cell*K19*x19*x6/(x6+k19*(1+x1/ki1+x3/ki2+x7/ks))||ks = 500.0; K19 = 3000.0; ki2 = 30.0; k19 = 160.0; ki1 = 0.3|
|x8 =>||cell*kd8*x8||kd8 = 0.1|
|=> x9; x8||kd8*x8*cell||kd8 = 0.1|
|x10 => x11; x24||cell*K24*x24*x10/(x10+k24*(1+x11/ks))||ks = 500.0; k24 = 70.0; K24 = 500.0|
|x10 => x12; x11, x21, x3, x5, x7||cell*K21*x21*x10/(x10+k21*(1+x5/ki7+x3/ki8+x7/ki11+x11/ki12+x12/ks))||k21 = 5.0; ks = 500.0; ki8 = 4.0; ki7 = 30.0; ki11 = 15.0; K21 = 5000.0; ki12 = 6.3|
(added: 23 Mar 2007, 20:57:51, updated: 23 Mar 2007, 20:57:51)