Quantitative systems modeling approaches towards model-informed drug development: Perspective through case studies

Quantitative systems pharmacology (QSP) modeling has become an increasingly popular approach impacting our understanding of disease mechanisms and helping predict patients’ treatment responses to facilitate study design or development go/no-go decisions. In this paper, we highlight the notable contr...

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Published inFrontiers in Systems Biology (Online) Vol. 2
Main Authors Verma, Meghna, Gall, Louis, Biasetti, Jacopo, Di Veroli, Giovanni Y., Pichardo-Almarza, Cesar, Gibbs, Megan A., Kimko, Holly
Format Journal Article
LanguageEnglish
Published Frontiers Media S.A 12.01.2023
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Abstract Quantitative systems pharmacology (QSP) modeling has become an increasingly popular approach impacting our understanding of disease mechanisms and helping predict patients’ treatment responses to facilitate study design or development go/no-go decisions. In this paper, we highlight the notable contributions and opportunities that QSP approaches are to offer during the drug development process by sharing three examples that have facilitated internal decisions. The barriers to successful applications and the factors that facilitate the success of the modeling approach is discussed.
AbstractList Quantitative systems pharmacology (QSP) modeling has become an increasingly popular approach impacting our understanding of disease mechanisms and helping predict patients’ treatment responses to facilitate study design or development go/no-go decisions. In this paper, we highlight the notable contributions and opportunities that QSP approaches are to offer during the drug development process by sharing three examples that have facilitated internal decisions. The barriers to successful applications and the factors that facilitate the success of the modeling approach is discussed.
Author Gall, Louis
Verma, Meghna
Pichardo-Almarza, Cesar
Gibbs, Megan A.
Biasetti, Jacopo
Kimko, Holly
Di Veroli, Giovanni Y.
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Cites_doi 10.1002/psp4.12403
10.1208/s12248-019-0339-5
10.1002/psp4.12282
10.1038/s41556-022-00899-8
10.1016/j.cotox.2017.07.003
10.1007/s10928-021-09790-9
10.1002/psp4.12390
10.1126/scisignal.aab0990
10.1016/j.ymthe.2020.11.015
10.1046/j.0960-7722.2001.00216.x
10.1002/psp4.12463
10.1016/j.bone.2009.08.053
10.1016/j.pbiomolbio.2014.06.010
10.1002/cphy.c150006
10.3389/fphar.2016.00414
10.1200/cci.18.00069
10.1002/psp4.12351
10.1186/s40425-018-0327-9
10.1007/s10928-021-09785-6
10.1073/pnas.082080899
10.1371/journal.pcbi.1001045
10.1002/psp4.12071
10.1016/j.jacbts.2019.02.006
10.1002/psp4.12381
10.1208/s12248-021-00580-2
10.1016/j.cpc.2009.07.019
10.1093/bib/bbp005
10.1016/j.phrs.2017.07.015
10.1038/nature24489
10.3390/pharmaceutics13071016
10.1039/c9lc01107b
10.3389/fphar.2014.00247
10.1186/gb-2008-9-12-328
10.1038/embor.2008.7
10.1016/j.celrep.2020.108633
10.1001/jamanetworkopen.2019.2535
10.3892/mmr.2019.10274
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References Knöchel (B21) 2022
Gadkar (B15) 2016; 5
Metzcar (B28) 2019; 3
Poch (B35) 2022; 24
McQuade (B26) 2016; 7
Pin (B33) 2021; 23
Peterson (B32) 2010; 46
Haber (B16) 2017; 551
Nijsen (B29) 2018; 7
Fleisher (B12) 2017; 124
Humeres (B19) 2019; 4
Riccio (B37) 2008; 9
Cheng (B7) 2022; 49
Bloomingdale (B3) 2017; 4
Buske (B6) 2011; 7
Bradshaw (B5) 2019; 8
Cucurull-Sanchez (B10) 2019; 8
Fey (B11) 2015; 8
Pitt-Francis (B34) 2009; 180
Foo (B13) 2021; 29
Meineke (B27) 2001; 34
Humeres (B18) 2019; 4
Aghamiri (B1) 2022; 49
Clausznitzer (B8) 2018; 7
Tan (B40) 2021; 34
Ramanujan (B36) 2016
Csikász-Nagy (B9) 2009; 10
Frangogiannis (B14) 2015; 5
Peter (B30) 2011
Haslam (B17) 2019; 2
Kosinsky (B22) 2018; 6
Peters (B31) 2020; 20
Bai (B2) 2019; 21
Sancho-Araiz (B39) 2021; 13
Kirouac (B20) 2019; 8
Zineh (B41) 2019; 8
Bonabeau (B4) 2002; 99
Leil (B23) 2014; 5
Loewe (B25) 2008; 9
Rouillard (B38) 2014; 115
Liu (B24) 2019; 20
References_xml – volume: 8
  start-page: 336
  year: 2019
  ident: B41
  article-title: Quantitative systems pharmacology: A regulatory perspective on translation
  publication-title: CPT Pharmacometrics Syst. Pharmacol.
  doi: 10.1002/psp4.12403
  contributor:
    fullname: Zineh
– volume: 21
  start-page: 72
  year: 2019
  ident: B2
  article-title: Translational quantitative systems pharmacology in drug development: From current landscape to good practices
  publication-title: AAPS J.
  doi: 10.1208/s12248-019-0339-5
  contributor:
    fullname: Bai
– volume: 7
  start-page: 135
  year: 2018
  ident: B29
  article-title: Preclinical QSP modeling in the pharmaceutical industry: An IQ consortium survey examining the current landscape
  publication-title: CPT Pharmacometrics Syst. Pharmacol.
  doi: 10.1002/psp4.12282
  contributor:
    fullname: Nijsen
– volume: 24
  start-page: 659
  year: 2022
  ident: B35
  article-title: Migratory and anti-fibrotic programmes define the regenerative potential of human cardiac progenitors
  publication-title: Nat. Cell Biol.
  doi: 10.1038/s41556-022-00899-8
  contributor:
    fullname: Poch
– volume: 4
  start-page: 79
  year: 2017
  ident: B3
  article-title: Quantitative systems toxicology
  publication-title: Curr. Opin. Toxicol.
  doi: 10.1016/j.cotox.2017.07.003
  contributor:
    fullname: Bloomingdale
– volume: 49
  start-page: 19
  year: 2022
  ident: B1
  article-title: Recent applications of quantitative systems pharmacology and machine learning models across diseases
  publication-title: J. Pharmacokinet. pharmacodynamics
  doi: 10.1007/s10928-021-09790-9
  contributor:
    fullname: Aghamiri
– volume: 8
  start-page: 205
  year: 2019
  ident: B20
  article-title: Reproducibility of quantitative systems pharmacology models: Current challenges and future opportunities
  publication-title: CPT Pharmacometrics Syst. Pharmacol.
  doi: 10.1002/psp4.12390
  contributor:
    fullname: Kirouac
– volume: 8
  start-page: ra130
  year: 2015
  ident: B11
  article-title: Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients
  publication-title: Sci. Signal.
  doi: 10.1126/scisignal.aab0990
  contributor:
    fullname: Fey
– volume: 29
  start-page: 409
  year: 2021
  ident: B13
  article-title: Human ISL1(+) ventricular progenitors self-assemble into an in vivo functional heart patch and preserve cardiac function post infarction
  publication-title: Mol. Ther. J. Am. Soc. Gene Ther.
  doi: 10.1016/j.ymthe.2020.11.015
  contributor:
    fullname: Foo
– year: 2011
  ident: B30
  article-title: Brian shoichet JLS, shankar subramaniam, piet van der Graaf and paolo vicini quantitative and systems pharmacology in the post-genomic era: New approaches to discovering drugs and understanding therapeutic mechanisms NIH white paper
  contributor:
    fullname: Peter
– volume: 34
  start-page: 253
  year: 2001
  ident: B27
  article-title: Cell migration and organization in the intestinal crypt using a lattice-free model
  publication-title: Cell Prolif.
  doi: 10.1046/j.0960-7722.2001.00216.x
  contributor:
    fullname: Meineke
– volume: 8
  start-page: 777
  year: 2019
  ident: B5
  article-title: Applications of quantitative systems pharmacology in model-informed drug discovery: Perspective on impact and opportunities
  publication-title: CPT Pharmacometrics Syst. Pharmacol.
  doi: 10.1002/psp4.12463
  contributor:
    fullname: Bradshaw
– volume: 46
  start-page: 49
  year: 2010
  ident: B32
  article-title: A physiologically based mathematical model of integrated calcium homeostasis and bone remodeling
  publication-title: Bone
  doi: 10.1016/j.bone.2009.08.053
  contributor:
    fullname: Peterson
– volume: 115
  start-page: 235
  year: 2014
  ident: B38
  article-title: Coupled agent-based and finite-element models for predicting scar structure following myocardial infarction
  publication-title: Prog. biophysics Mol. Biol.
  doi: 10.1016/j.pbiomolbio.2014.06.010
  contributor:
    fullname: Rouillard
– volume: 5
  start-page: 1841
  year: 2015
  ident: B14
  article-title: Pathophysiology of myocardial infarction
  publication-title: Compr. Physiol.
  doi: 10.1002/cphy.c150006
  contributor:
    fullname: Frangogiannis
– volume-title: Quantitative systems pharmacology: Applications and adoption in drug development. Systems pharmacology and pharmacodynamics
  year: 2016
  ident: B36
  contributor:
    fullname: Ramanujan
– volume: 7
  start-page: 414
  year: 2016
  ident: B26
  article-title: Chemotherapy-induced constipation and diarrhea: Pathophysiology, current and emerging treatments
  publication-title: Curr. Emerg. Treat.
  doi: 10.3389/fphar.2016.00414
  contributor:
    fullname: McQuade
– volume: 3
  start-page: 1
  year: 2019
  ident: B28
  article-title: A review of cell-based computational modeling in cancer biology
  publication-title: JCO Clin. cancer Inf.
  doi: 10.1200/cci.18.00069
  contributor:
    fullname: Metzcar
– volume: 7
  start-page: 759
  year: 2018
  ident: B8
  article-title: Quantitative systems pharmacology model for alzheimer disease indicates targeting sphingolipid dysregulation as potential treatment option
  publication-title: CPT Pharmacometrics Syst. Pharmacol.
  doi: 10.1002/psp4.12351
  contributor:
    fullname: Clausznitzer
– volume: 6
  start-page: 17
  year: 2018
  ident: B22
  article-title: Radiation and PD-(L)1 treatment combinations: Immune response and dose optimization via a predictive systems model
  publication-title: J. Immunother. cancer
  doi: 10.1186/s40425-018-0327-9
  contributor:
    fullname: Kosinsky
– volume: 49
  start-page: 39
  year: 2022
  ident: B7
  article-title: Review of applications and challenges of quantitative systems pharmacology modeling and machine learning for heart failure
  publication-title: J. Pharmacokinet. pharmacodynamics
  doi: 10.1007/s10928-021-09785-6
  contributor:
    fullname: Cheng
– volume: 99
  start-page: 7280
  year: 2002
  ident: B4
  article-title: Agent-based modeling: Methods and techniques for simulating human systems
  publication-title: Proc. Natl. Acad. Sci. U. S. A.
  doi: 10.1073/pnas.082080899
  contributor:
    fullname: Bonabeau
– volume: 7
  start-page: e1001045
  year: 2011
  ident: B6
  article-title: A comprehensive model of the spatio-temporal stem cell and tissue organisation in the intestinal crypt
  publication-title: PLoS Comput. Biol.
  doi: 10.1371/journal.pcbi.1001045
  contributor:
    fullname: Buske
– volume: 5
  start-page: 235
  year: 2016
  ident: B15
  article-title: A six-stage workflow for robust application of systems pharmacology
  publication-title: CPT Pharmacometrics Syst. Pharmacol.
  doi: 10.1002/psp4.12071
  contributor:
    fullname: Gadkar
– volume: 4
  start-page: 449
  year: 2019
  ident: B19
  article-title: Fibroblasts in the infarcted, remodeling, and failing heart
  publication-title: JACC Basic Transl. Sci.
  doi: 10.1016/j.jacbts.2019.02.006
  contributor:
    fullname: Humeres
– volume: 8
  start-page: 259
  year: 2019
  ident: B10
  article-title: Best practices to maximize the use and reuse of quantitative and systems pharmacology models: Recommendations from the United Kingdom quantitative and systems pharmacology network
  publication-title: CPT Pharmacometrics Syst. Pharmacol.
  doi: 10.1002/psp4.12381
  contributor:
    fullname: Cucurull-Sanchez
– volume: 23
  start-page: 77
  year: 2021
  ident: B33
  article-title: Systems modeling to quantify safety risks in early drug development: Using bifurcation analysis and agent-based modeling as examples
  publication-title: AAPS J.
  doi: 10.1208/s12248-021-00580-2
  contributor:
    fullname: Pin
– start-page: 1569
  volume-title: CPT: pharmacometrics & systems pharmacology
  year: 2022
  ident: B21
  article-title: A case-study of model-informed drug development of a novel PCSK9 anti sense oligonucleotide. Part 1: First time in man to phase II
  contributor:
    fullname: Knöchel
– volume: 180
  start-page: 2452
  year: 2009
  ident: B34
  article-title: Chaste: A test-driven approach to software development for biological modelling
  doi: 10.1016/j.cpc.2009.07.019
  contributor:
    fullname: Pitt-Francis
– volume: 10
  start-page: 424
  year: 2009
  ident: B9
  article-title: Computational systems biology of the cell cycle
  publication-title: Briefings Bioinforma.
  doi: 10.1093/bib/bbp005
  contributor:
    fullname: Csikász-Nagy
– volume: 124
  start-page: 20
  year: 2017
  ident: B12
  article-title: Application of pharmacometrics and quantitative systems pharmacology to cancer therapy: The example of luminal a breast cancer
  publication-title: Pharmacol. Res.
  doi: 10.1016/j.phrs.2017.07.015
  contributor:
    fullname: Fleisher
– volume: 4
  start-page: 449
  year: 2019
  ident: B18
  article-title: Fibroblasts in the infarcted, remodeling, and failing heart
  publication-title: JACC Basic Transl. Sci.
  doi: 10.1016/j.jacbts.2019.02.006
  contributor:
    fullname: Humeres
– volume: 551
  start-page: 333
  year: 2017
  ident: B16
  article-title: A single-cell survey of the small intestinal epithelium
  publication-title: Nature
  doi: 10.1038/nature24489
  contributor:
    fullname: Haber
– volume: 13
  start-page: 1016
  year: 2021
  ident: B39
  article-title: The role of mathematical models in immuno-oncology: Challenges and future perspectives
  publication-title: Pharmaceutics
  doi: 10.3390/pharmaceutics13071016
  contributor:
    fullname: Sancho-Araiz
– volume: 20
  start-page: 1177
  year: 2020
  ident: B31
  article-title: Developing in vitro assays to transform gastrointestinal safety assessment: Potential for microphysiological systems
  publication-title: Lab a chip
  doi: 10.1039/c9lc01107b
  contributor:
    fullname: Peters
– volume: 5
  start-page: 247
  year: 2014
  ident: B23
  article-title: Quantitative Systems Pharmacology can reduce attrition and improve productivity in pharmaceutical research and development
  publication-title: Front. Pharmacol.
  doi: 10.3389/fphar.2014.00247
  contributor:
    fullname: Leil
– volume: 9
  start-page: 328
  year: 2008
  ident: B25
  article-title: Computational models in systems biology
  publication-title: Genome Biol.
  doi: 10.1186/gb-2008-9-12-328
  contributor:
    fullname: Loewe
– volume: 9
  start-page: 377
  year: 2008
  ident: B37
  article-title: Loss of intestinal crypt progenitor cells owing to inactivation of both Notch1 and Notch2 is accompanied by derepression of CDK inhibitors p27Kip1 and p57Kip2
  publication-title: EMBO Rep.
  doi: 10.1038/embor.2008.7
  contributor:
    fullname: Riccio
– volume: 34
  start-page: 108633
  year: 2021
  ident: B40
  article-title: A constant pool of Lgr5+ intestinal stem cells is required for intestinal homeostasis
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2020.108633
  contributor:
    fullname: Tan
– volume: 2
  start-page: e192535
  year: 2019
  ident: B17
  article-title: Estimation of the percentage of US patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs
  publication-title: JAMA Netw. Open
  doi: 10.1001/jamanetworkopen.2019.2535
  contributor:
    fullname: Haslam
– volume: 20
  start-page: 473
  year: 2019
  ident: B24
  article-title: Paneth cell ablation increases the small intestinal injury during acute necrotizing pancreatitis in rats
  publication-title: Mol. Med. Rep.
  doi: 10.3892/mmr.2019.10274
  contributor:
    fullname: Liu
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SubjectTerms Computational modeling
model informed drug development
Quantitative systems pharmacology
quantitative systems toxicology
systems modeling
Title Quantitative systems modeling approaches towards model-informed drug development: Perspective through case studies
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