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Utility of constraints reflecting system stability on analyses for biological models

Simulating complex biological models consisting of multiple ordinary differential equations can aid in the prediction of the pharmacological/biological responses; however, they are often hampered by the availability of reliable kinetic parameters. In the present study, we aimed to discover the prope...

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Autores principales: Kariya, Yoshiaki, Honma, Masashi, Tokuda, Keita, Konagaya, Akihiko, Suzuki, Hiroshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491612/
https://www.ncbi.nlm.nih.gov/pubmed/36084151
http://dx.doi.org/10.1371/journal.pcbi.1010441
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author Kariya, Yoshiaki
Honma, Masashi
Tokuda, Keita
Konagaya, Akihiko
Suzuki, Hiroshi
author_facet Kariya, Yoshiaki
Honma, Masashi
Tokuda, Keita
Konagaya, Akihiko
Suzuki, Hiroshi
author_sort Kariya, Yoshiaki
collection PubMed
description Simulating complex biological models consisting of multiple ordinary differential equations can aid in the prediction of the pharmacological/biological responses; however, they are often hampered by the availability of reliable kinetic parameters. In the present study, we aimed to discover the properties of behaviors without determining an optimal combination of kinetic parameter values (parameter set). The key idea was to collect as many parameter sets as possible. Given that many systems are biologically stable and resilient (BSR), we focused on the dynamics around the steady state and formulated objective functions for BSR by partial linear approximation of the focused region. Using the objective functions and modified global cluster Newton method, we developed an algorithm for a thorough exploration of the allowable parameter space for biological systems (TEAPS). We first applied TEAPS to the NF-κB signaling model. This system shows a damped oscillation after stimulation and seems to fit the BSR constraint. By applying TEAPS, we found several directions in parameter space which stringently determines the BSR property. In such directions, the experimentally fitted parameter values were included in the range of the obtained parameter sets. The arachidonic acid metabolic pathway model was used as a model related to pharmacological responses. The pharmacological effects of nonsteroidal anti-inflammatory drugs were simulated using the parameter sets obtained by TEAPS. The structural properties of the system were partly extracted by analyzing the distribution of the obtained parameter sets. In addition, the simulations showed inter-drug differences in prostacyclin to thromboxane A2 ratio such that aspirin treatment tends to increase the ratio, while rofecoxib treatment tends to decrease it. These trends are comparable to the clinical observations. These results on real biological models suggest that the parameter sets satisfying the BSR condition can help in finding biologically plausible parameter sets and understanding the properties of biological systems.
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spelling pubmed-94916122022-09-22 Utility of constraints reflecting system stability on analyses for biological models Kariya, Yoshiaki Honma, Masashi Tokuda, Keita Konagaya, Akihiko Suzuki, Hiroshi PLoS Comput Biol Research Article Simulating complex biological models consisting of multiple ordinary differential equations can aid in the prediction of the pharmacological/biological responses; however, they are often hampered by the availability of reliable kinetic parameters. In the present study, we aimed to discover the properties of behaviors without determining an optimal combination of kinetic parameter values (parameter set). The key idea was to collect as many parameter sets as possible. Given that many systems are biologically stable and resilient (BSR), we focused on the dynamics around the steady state and formulated objective functions for BSR by partial linear approximation of the focused region. Using the objective functions and modified global cluster Newton method, we developed an algorithm for a thorough exploration of the allowable parameter space for biological systems (TEAPS). We first applied TEAPS to the NF-κB signaling model. This system shows a damped oscillation after stimulation and seems to fit the BSR constraint. By applying TEAPS, we found several directions in parameter space which stringently determines the BSR property. In such directions, the experimentally fitted parameter values were included in the range of the obtained parameter sets. The arachidonic acid metabolic pathway model was used as a model related to pharmacological responses. The pharmacological effects of nonsteroidal anti-inflammatory drugs were simulated using the parameter sets obtained by TEAPS. The structural properties of the system were partly extracted by analyzing the distribution of the obtained parameter sets. In addition, the simulations showed inter-drug differences in prostacyclin to thromboxane A2 ratio such that aspirin treatment tends to increase the ratio, while rofecoxib treatment tends to decrease it. These trends are comparable to the clinical observations. These results on real biological models suggest that the parameter sets satisfying the BSR condition can help in finding biologically plausible parameter sets and understanding the properties of biological systems. Public Library of Science 2022-09-09 /pmc/articles/PMC9491612/ /pubmed/36084151 http://dx.doi.org/10.1371/journal.pcbi.1010441 Text en © 2022 Kariya et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kariya, Yoshiaki
Honma, Masashi
Tokuda, Keita
Konagaya, Akihiko
Suzuki, Hiroshi
Utility of constraints reflecting system stability on analyses for biological models
title Utility of constraints reflecting system stability on analyses for biological models
title_full Utility of constraints reflecting system stability on analyses for biological models
title_fullStr Utility of constraints reflecting system stability on analyses for biological models
title_full_unstemmed Utility of constraints reflecting system stability on analyses for biological models
title_short Utility of constraints reflecting system stability on analyses for biological models
title_sort utility of constraints reflecting system stability on analyses for biological models
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491612/
https://www.ncbi.nlm.nih.gov/pubmed/36084151
http://dx.doi.org/10.1371/journal.pcbi.1010441
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