Reaction Mechanisms and Kinetic Constants used in Mechanistic Models of Coagulation and Fibrinolysis
Mathematical modelling of natural phenomena, Tome 11 (2016) no. 6, pp. 71-90.

Voir la notice de l'article provenant de la source EDP Sciences

Computational modeling has gained a strong foothold as a tool for understanding and simulating biological phenomena like blood coagulation. However, exceptional complexity of these phenomena (that include hundreds of individual biochemical processes and a few biophysical processes) complicates development of reliable models and interpretation of the results. It is thus of great importance that a model of hemostasis designed for a particular application should be reproducible, apart from making robust predictions. Such a model would further reflect useful pharmacological implications not only with respect to identifying drug targets but also in understanding drug effects on their respective targets. We show, using a sample model, that model predictions vary significantly with the use of different values available in the literature for the same kinetic constant. We thus highlight the importance of having consensus of kinetic constants used in the formulation of mechanistic models for coagulation, and document values for each kinetic constant that can be used in such models, and for varying reaction conditions (synthetic, in vitro, in vivo).
DOI : 10.1051/mmnp/201611605

A.M. Susree 1 ; B.M. Anand 1

1 Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, Telangana, INDIA
@article{MMNP_2016_11_6_a4,
     author = {A.M. Susree and B.M. Anand},
     title = {Reaction {Mechanisms} and {Kinetic} {Constants} used in {Mechanistic} {Models} of {Coagulation} and {Fibrinolysis}},
     journal = {Mathematical modelling of natural phenomena},
     pages = {71--90},
     publisher = {mathdoc},
     volume = {11},
     number = {6},
     year = {2016},
     doi = {10.1051/mmnp/201611605},
     language = {en},
     url = {https://geodesic-test.mathdoc.fr/articles/10.1051/mmnp/201611605/}
}
TY  - JOUR
AU  - A.M. Susree
AU  - B.M. Anand
TI  - Reaction Mechanisms and Kinetic Constants used in Mechanistic Models of Coagulation and Fibrinolysis
JO  - Mathematical modelling of natural phenomena
PY  - 2016
SP  - 71
EP  - 90
VL  - 11
IS  - 6
PB  - mathdoc
UR  - https://geodesic-test.mathdoc.fr/articles/10.1051/mmnp/201611605/
DO  - 10.1051/mmnp/201611605
LA  - en
ID  - MMNP_2016_11_6_a4
ER  - 
%0 Journal Article
%A A.M. Susree
%A B.M. Anand
%T Reaction Mechanisms and Kinetic Constants used in Mechanistic Models of Coagulation and Fibrinolysis
%J Mathematical modelling of natural phenomena
%D 2016
%P 71-90
%V 11
%N 6
%I mathdoc
%U https://geodesic-test.mathdoc.fr/articles/10.1051/mmnp/201611605/
%R 10.1051/mmnp/201611605
%G en
%F MMNP_2016_11_6_a4
A.M. Susree; B.M. Anand. Reaction Mechanisms and Kinetic Constants used in Mechanistic Models of Coagulation and Fibrinolysis. Mathematical modelling of natural phenomena, Tome 11 (2016) no. 6, pp. 71-90. doi : 10.1051/mmnp/201611605. https://geodesic-test.mathdoc.fr/articles/10.1051/mmnp/201611605/

[1] Te Adams, Sj Everse, Kg Mann Predicting the pharmacology of thrombin inhibitors Journal of Thrombosis and Haemostasis 1024 1027 2003

[2] S S Ahmad, P N Walsh Platelet membrane-mediated coagulation protease complex assembly Trends in cardiovascular medicine 271 278 1994

[3] S S Ahmad, R Rawala-Sheikh, B Ashby, P N Walsh Platelet receptor-mediated factor x activation by factor ixa. high-affinity factor ixa receptors induced by factor viii are deficient on platelets in scott syndrome Journal of Clinical Investigation 824 1989

[4] S S Ahmad, F S London, P N Walsh The assembly of the factor x-activating complex on activated human platelets Journal of Thrombosis and Haemostasis 48 59 2003

[5] M Anand, K Rajagopal, K R Rajagopal A model incorporating some of the mechanical and biochemical factors underlying clot formation and dissolution in flowing blood Journal of Theoretical Medicine 183 218 2003

[6] M Anand, K Rajagopal, K R Rajagopal A model for the formation, growth, and lysis of clots in quiescent plasma. a comparison between the effects of antithrombin iii deficiency and protein c deficiency Journal of Theoretical Biology 725 738 2008

[7] F I Ataullakhanov, V I Zarnitsina, A V Pokhilko, A I Lobanov, O L Morozova Spatio-temporal dynamics of blood coagulation and pattern formation: a theoretical approach International Journal of Bifurcation and Chaos 1985 2002a

[8] F I Ataullakhanov, V I Zarnitsina, A V Pokhilko, A I Lobanov, O L Morozova Spatio-temporal dynamics of blood coagulation and pattern formation: a theoretical approach International Journal of Bifurcation and Chaos 1985 2002 2002b

[9] S P Bajaj, S I Rapaport, S F Brown Isolation and characterization of human factor vii. activation of factor vii by factor xa Journal of Biological Chemistry 253 259 1981

[10] L Bajzar Thrombin activatable fibrinolysis inhibitor and an antifibrinolytic pathway Arteriosclerosis, thrombosis, and vascular biology 2511 2518 2000

[11] A N Balandina, A M Shibeko, D A Kireev, A A Novikova, I I Shmirev, M A Panteleev, F I Ataullakhanov Positive feedback loops for factor v and factor vii activation supply sensitivity to local surface tissue factor density during blood coagulation Biophysical journal 1816 1824 2011

[12] K A Bauer, B L Kass, H Ten Cate, J J Hawiger, R D Rosenberg Factor ix is activated in vivo by the tissue factor mechanism Blood 731 736 1990

[13] R J Baugh, G J Broze, S Krishnaswamy Regulation of Extrinsic Pathway Factor Xa Formation by Tissue Factor Pathway Inhibitor Journal of Biological Chemistry 4378 4386 1998

[14] T Bodnar, A Sequeira Numerical Simulation of the Coagulation Dynamics of Blood Computational and Mathematical Methods in Medicine 83 104 2008

[15] T Bodnaar, A Fasano, and A Sequeira. Mathematical models for blood coagulation. In Fluid-Structure Interaction and Biomedical Applications, pages 483–569. Springer, 2014.

[16] K Brummel-Ziedins Models for thrombin generation and risk of disease Journal of Thrombosis and Haemostasis 212 223 2013

[17] S D Bungay, P A Gentry, R D Gentry A mathematical model of lipid-mediated thrombin generation Mathematical Medicine and Biology 105 129 2003

[18] Rolf Burghaus, Katrin Coboeken, Thomas Gaub, Lars Kuepfer, Anke Sensse, Hans-Ulrich Siegmund, Wolfgang Weiss, Wolfgang Mueck, Joerg Lippert Evaluation of the efficacy and safety of rivaroxaban using a computer model for blood coagulation PLoS One e17626 2011

[19] S Butenas, K G Mann Kinetics of human factor vii activation Biochemistry 1904 1910 1996

[20] S Butenas, K G Mann Blood coagulation Biochemistry (Moscow) 3 12 2002

[21] M S Chatterjee, W S Denney, H Jing, S L Diamond Systems biology of coagulation initiation: kinetics of thrombin generation in resting and activated human blood PLoS Computational Biology e1000950 2010

[22] S D Conte and C W De Boor. Elementary numerical analysis: an algorithmic approach. McGraw-Hill Higher Education, 1980.

[23] C M Danforth, T Orfeo, K G Mann, K E Brummel-Ziedins, S J Everse The impact of uncertainty in a blood coagulation model Mathematical Medicine and Biology 323 336 2009

[24] R De Cristofaro, V De Filippis Interaction of the 268-282 region of glycoprotein ibalpha with the heparin-binding site of thrombin inhibits the enzyme activation of factor viii Biochemical Journal 593 601 2003

[25] P De Moerloose, H R Bounameaux, P M Mannucci Screening test for thrombophilic patients: which tests, for which patient, by whom, when, and why? In Seminars in thrombosis and hemostasis 321 327 1997

[26] S L Diamond Systems biology of coagulation Journal of Thrombosis and Haemostasis 224 232 2013

[27] S L Diamond, S Anand Inner clot diffusion and permeation during fibrinolysis Biophysical journal 2622 1993

[28] C T Esmon, W G Owen, C M Jackson The Conversion of Prothrombin to Thrombin Journal of Biological Chemistry 7798 7807 1974

[29] P J Fay, T L Beattie, L M Regan, L M O Brien, R J Kaufman Model for the Factor VIIIa-dependent Decay of the Intrinsic Factor Xase: Role of Subunit Dissociation and Factor IXa-Catalyzed Proteolysis Journal of Biological Chemistry 6027 6032 1996

[30] A L Fogelson, Y H Hussain, K Leiderman Blood clot formation under flow: the importance of factor xi depends strongly on platelet count Biophysical journal 10 18 2012

[31] J H Foley, P F Cook, M E Nesheim Kinetics of activated thrombin-activatable fibrinolysis inhibitor (tafia)-catalyzed cleavage of c-terminal lysine residues of fibrin degradation products and removal of plasminogen-binding sites Journal of Biological Chemistry 19280 19286 2011

[32] J M Freyssinet, F Toti-Orfanoudakis, C Ravanat, L Grunebaum, J Gauchy, J P Cazenave, M L Wiesel The catalytic role of anionic phospholipids in the activation of protein c by factor xa and expression of its anticoagulant function in human plasma Blood Coagulation & Fibrinolysis 691 1991

[33] B Furie, B C Furie Mechanisms of thrombus formation New England Journal of Medicine 938 949 2008

[34] D Gailani, G J Broze Factor xi activation in a revised model of blood coagulation Science 909 912 1991

[35] D Gailani, D Ho, M Sun, Q Cheng, P N Walsh Model for a factor IX activation complex on blood platelets : dimeric conformation of factor XIa is essential Blood 3117 3123 2001

[36] A Gulati, Gk Isbister, Sb Duffull Scale reduction of a systems coagulation model with an application to modeling pharmacokinetic-pharmacodynamic data CPT: pharmacometrics & systems pharmacology 1 8 2014

[37] L M Haynes, Y C Dubief, T Orfeo, K G Mann Dilutional control of prothrombin activation at physiologically relevant shear rates Biophysical journal 765 773 2011

[38] L M Haynes, Y C Dubief, K G Mann Membrane binding events in the initiation and propagation phases of tissue factor-initiated zymogen activation under flow Journal of Biological Chemistry 5225 5234 2012

[39] M J Heeb, R Bischoff, M Courtney, J H Griffin Inhibition of activated protein c by recombinant alpha 1-antitrypsin variants with substitution of arginine or leucine for methionine358 Journal of Biological Chemistry 2365 2369 1990

[40] H C Hemker, F I Ataullakhanov Good mathematical practice: simulation of the hemostatic-thrombotic mechanism, a powerful tool but one that must be used with circumspection Pathophysiology of haemostasis and thrombosis 55 57 2005

[41] H C Hemker, S Kerdelo, R M W Kremers Is there value in kinetic modeling of thrombin generation ? No ( unless… ) Journal of Thrombosis and Haemostasis 1470 1477 2012

[42] D C Hill-Eubanks, P Lollar von willebrand factor is a cofactor for thrombin-catalyzed cleavage of the factor viii light chain Journal of Biological Chemistry 17854 17858 1990

[43] M F Hockin, K C Jones, S J Everse, K G Mann A model for the stoichiometric regulation of blood coagulation Journal of Biological Chemistry 18322 18333 2002

[44] R Hoffman, E J Benz, L E Silberstein, H Heslop, J Weitz, and J Anastasi. Hematology: Basic Principles and Practice, Expert Consult Premium Edition - Enhanced Online Features. Elsevier Health Sciences, 2012. ISBN 9781455740413.

[45] K C Jones, K G Mann A Model for the Tissue Factor Pathway to Thrombin Journal of Biological Chemistry 23367 23373 1994

[46] K Kolev, I Lerant, K Tenekejiev, R Machovich Regulation of fibrinolytic activity of neutrophil leukocyte elastase, plasmin, and miniplasmin by plasma protease inhibitors Journal of Biological Chemistry 17030 17034 1994

[47] Yutaka Komiyama, Anders H Pedersen, Walter Kisiel Proteolytic activation of human factors ix and x by recombinant human factor viia: effects of calcium, phospholipids, and tissue factor Biochemistry 9418 9425 1990

[48] S Krishnaswamy The interaction of human factor viia with tissue factor Journal of Biological Chemistry 23696 23706 1992

[49] S Krishnaswamy, W R Church, M E Nesheim, K G Mann Activation of Human Prothrombin Journal of Biological Chemistry 3291 3299 1987

[50] S Krishnaswamy, K C Jones, K G Mann Prothrombinase complex assembly. kinetic mechanism of enzyme assembly on phospholipid vesicles Journal of Biological Chemistry 3823 3834 1988

[51] S Krishnaswamy, K A Field, T S Edgington, J H Morrissey, K G Mann Role of the Membrane Surface in the Activation of Human Coagulation Factor X Journal of Biological Chemistry 26110 26120 1992

[52] A L Kuharsky, A L Fogelson Surface-mediated control of blood coagulation: the role of binding site densities and platelet deposition Biophysical journal 1050 1074 2001

[53] D E Lacroix, M Anand A model for the formation, growth, and dissolution of clots in vitro. effect of the intrinsic pathway on antithrombin iii deficiency and protein c deficiency International journal of advances in engineering sciences and applied mathematics 93 105 2011

[54] J H Lawson, S Butenas, N Ribarik Complex-dependent Inhibition of Factor VIIa by Antithrombin III and Heparin Journal of Biological Chemistry 767 770 1993

[55] K Leiderman, A Fogelson An overview of mathematical modeling of thrombus formation under flow Thrombosis Research S12 S14 2014

[56] R J Leipold, T A Bozarth, A L Racanelli, I B Dicker Mathematical Model of Serine Protease Inhibition in the Tissue Factor Pathway to Thrombin Journal of Biological Chemistry 25383 25387 1995

[57] K Lo, W S Denney, S L Diamond Stochastic modeling of blood coagulation initiation Pathophysiology of haemostasis and thrombosis 80 90 2005

[58] P Lollar, G J Knutson, D N Fass Activation of porcine factor viii: C by thrombin and factor xa Biochemistry 8056 8064 1985

[59] C Longstaff, C Thelwell Understanding the enzymology of fibrinolysis and improving thrombolytic therapy FEBS letters 3303 3309 2005

[60] D Luan, M Zai, J D Varner Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies PLoS Computational Biology e142 2007

[61] D Luan, F Szlam, K A Tanaka, P S Barie, J D Varner Ensembles of uncertain mathematical models can identify network response to therapeutic interventions Molecular Biosystems 2272 2286 2010

[62] E L Madison, G S Coombs, D R Corey Substrate specificity of tissue type plasminogen activator characterization of the fibrin independent specificity of t-pa for plasminogen Journal of Biological Chemistry 7558 7562 1995

[63] K G Mann Thrombin formation CHEST Journal 4S 10S 2003

[64] K G Mann Is there value in kinetic modeling of thrombin generation? yes Journal of Thrombosis and Haemostasis 1463 1469 2012

[65] K G Mann, M E Nesheim, W R Church, P Haley, S Krishnaswamy Surface-dependent reactions of the vitamin k-dependent enzyme complexes Blood 1 16 1990

[66] K G Mann, K Brummel-Ziedins, T Orfeo, S Butenas Models of blood coagulation Blood Cells, Molecules, and Diseases 108 117 2006

[67] D D Monkovic, P B Tracy Activation of Human Factor V by Factor Xa and Thrombin Biochemistry 1118 1128 1990a

[68] D D Monkovic, P B Tracy Functional characterization of human platelet-released factor V and its activation by factor Xa and thrombin Journal of Biological Chemistry 17132 17140 1990b

[69] D M Monroe, M Hoffman, H R Roberts Platelets and thrombin generation Arteriosclerosis, thrombosis, and vascular biology 1381 1389 2002

[70] P P Naidu, M Anand Importance of viiia inactivation in a mathematical model for the formation, growth, and lysis of clots Mathematical Modelling of Natural Phenomena 17 33 2014

[71] P F Neuenschwander, J Jesty A Comparison of Phospholipid and Platelets in the Activation of Human Factor VIII by Thrombin and Factor Xa, and in the Activation of Factor X Blood 1761 1770 1988

[72] P F Neuenschwander, J Jesty Thrombin-activated and factor xa-activated human factor viii: differences in cofactor activity and decay rate Archives of biochemistry and biophysics 426 434 1992

[73] D P O'Brien, G Kemball-Cook, A M Hutchinson, Dma Martin, D J D Johnson, P G H Byfield, O Takamiya, E G D Tuddenham, J H Mcvey Surface plasmon resonance studies of the interaction between factor vii and tissue factor. demonstration of defective tissue factor binding in a variant fvii molecule (fvii-r79q) Biochemistry 14162 14169 1994

[74] L M O'Brien, M Mastri, P J Fay Regulation of factor viiia by human activated protein c and protein s: inactivation of cofactor in the intrinsic factor xase Blood 1714 1720 2000

[75] T Orfeo, K G Mann Mathematical and biological models of blood coagulation Journal of Thrombosis and Haemostasis 2397 2398 2005

[76] M A Panteleev, M V Ovanesov, D A Kireev, A M Shibeko, E I Sinauridze, N M Ananyeva, A A Butylin, E L Saenko, F I Ataullakhanov Spatial propagation and localization of blood coagulation are regulated by intrinsic and protein c pathways, respectively Biophysical Journal 1489 1500 2006

[77] M A Panteleev, N M Ananyeva, F I Ataullakhanov, E L Saenko Mathematical models of blood coagulation and platelet adhesion: clinical applications Current pharmaceutical design 1457 1467 2007

[78] R A Pixley, M Schapira, R W Colman The regulation of human factor xiia by plasma proteinase inhibitors Journal of Biological Chemistry 1723 1729 1985

[79] S I Rapaport The extrinsic pathway inhibitor: a regulator of tissue factor-dependent blood coagulation Thrombosis and haemostasis 6 15 1991

[80] S Raut, L Weller, T W Barrowcliffe Phospholipid binding of factor viii in different therapeutic concentrates British journal of haematology 323 329 1999

[81] R Rawala-Sheikh, S S Ahmad, B Ashby, P N Walsh Kinetics of Coagulation Factor X Activation by Platelet-Bound Factor IXa Biochemistry 2606 2611 1990

[82] D C Rijken, H R Lijnen New insights into the molecular mechanisms of the fibrinolytic system Journal of Thrombosis and Haemostasis 4 13 2009

[83] R D Rosenberg, J S Rosenberg Natural anticoagulant mechanisms Journal of Clinical Investigation 1 1984

[84] J Rosing, J L Van Rijn, E M Bevers, G Van Dieijen, P Comfurius, R F Zwaal The role of activated human platelets in prothrombin and factor x activation Blood 1985

[85] C F Scott, M Schapira, H L James, A B Cohen, R W Colman Inactivation of factor xia by plasma protease inhibitors: Predominant role of a1-protease inhibitor and protective effect of high molecular weight kininogen Journal of Clinical Investigation 844 1982

[86] A M Shibeko, E S Lobanova, M A Panteleev, F I Ataullakhanov Blood flow controls coagulation onset via the positive feedback of factor vii activation by factor xa BMC systems biology 1 2010

[87] J Shobe, C D Dickinson, T S Edgington, W Ruf Macromolecular Substrate Affinity for the Tissue Factor-Factor VIIa Complex Is Independent of Scissile Bond Docking Journal of Biological Chemistry 24171 24175 1999

[88] M Silverberg, A P Kaplan Enzymatic activities of activated and zymogen forms of human hageman factor (factor xii) Blood 64 70 1982

[89] S Solymoss, M M Tucker, P B Tracy Kinetics of inactivation of membrane-bound factor va by activated protein c. protein s modulates factor xa protection Journal of Biological Chemistry 14884 14890 1988

[90] H Soons, T Janssen-Claessen, G Tans, H C Hemker Inhibition of factor xia by antithrombin iii Biochemistry 4624 4629 1987

[91] Y Sun, D Gailani Identification of a factor ix binding site on the third apple domain of activated factor xi Journal of Biological Chemistry 29023 29028 1996

[92] M Susree and M Anand. A mathematical model for in vitro coagulation of blood: Role of platelet count inhibition. Sadhana, Accepted, 2016.

[93] N A Swords, K G Mann The assembly of the prothrombinase complex on adherent platelets Arteriosclerosis, Thrombosis, and Vascular Biology 1602 1612 1993

[94] D L Tankersley, J S Finlayson Kinetics of activation and autoactivation of human factor xii Biochemistry 273 279 1984

[95] M Tomaiuolo, T J Stalker, J D Welsh, S L Diamond, T Sinno, L F Brass A systems approach to hemostasis: 2. computational analysis of molecular transport in the thrombus microenvironment Blood 1816 1823 2014

[96] P B Tracy, K G Mann Prothrombinase complex assembly on the platelet surface is mediated through the 74,000-dalton component of factor va Proceedings of the National Academy of Sciences 2380 2384 1983

[97] M Tsiang, L R Paborsky, W X Li, A K Jain, C T Mao, K E Dunn, D W Lee, S Y Matsumura, M D Matteucci, S E Coutre, L L Leung Protein engineering thrombin for optimal specificity and potency of anticoagulant activity in vivo Biochemistry 16449 16457 1996

[98] F Van Der Graaf, J A Koedam, B N Bouma Inactivation of kallikrein in human plasma Journal of Clinical Investigation 149 1983

[99] G Van Dieijen, J L Van Rijn, J W Govers-Riemslag, H C Hemker, J Rosing Assembly of the intrinsic factor x activating complex-interactions between factor ixa, factor viiia and phospholipid Thrombosis and haemostasis 396 400 1985

[100] C Van'T Veer, K G Mann Regulation of tissue factor initiated thrombin generation by the stoichiometric inhibitors tissue factor pathway inhibitor, antithrombin-iii, and heparin cofactor-ii Journal of Biological Chemistry 4367 4377 1997

[101] F Varfaj, J Neuberg, P V Jenkins, H Wakabayashi, P J Fay Role of p1 residues arg336 and arg562 in the activated- protein-c-catalysed inactivation of factor viiia Biochemical Journal 355 362 2006

[102] P N Walsh, H Bradford, D Sinha, J R Piperno, G P Tuszynski Kinetics of the factor xia catalyzed activation of human blood coagulation factor ix Journal of Clinical Investigation 1392 1984

[103] Peter N Walsh Platelet coagulation-protein interactions Seminars in thrombosis and hemostasis 461 471 2004

[104] E M Wiebe, A R Stafford, C James, J I Weitz, J C Fredenburgh Mechanism of Catalysis of Inhibition of Factor IXa by Antithrombin in the Presence of Heparin or Pentasaccharide Journal of Biological Chemistry 35767 35774 2003

[105] G M Willems, T Lindhout, W Th Hermens, H C Hernkers Simulation Model for Thrombin Generation in Plasma Haemostasis 197 207 1991

[106] Z Xu, O Kim, M Kamocka, E D Rosen, M Alber Multiscale models of thrombogenesis Wiley Interdisciplinary Reviews: Systems Biology and Medicine 237 246 2012

[107] X Zhou, Drh Huntjens, Rahj Gilissen A systems pharmacology model for predicting effects of factor xa inhibitors in healthy subjects: Assessment of pharmacokinetics and binding kinetics CPT: pharmacometrics & systems pharmacology 650 659 2015

[108] M Zur, Y Nemerson Kinetics of Factor IX Activation via the Extrinsic Pathway Journal of Biological Chemistry 5703 5707 1979

Cité par Sources :