(M-021) An open-source and modular workflow for prototyping bispecific T-cell engager safety modules and integrating them into PBPK models

Alexander KULESZA – ESQlabs GmbH; Venetia Karamitsou – ESQlabs; Wilbert De Witte – ESQLabs; Matthias König – Humboldt-University Berlin; Stephan Schaller – ESQlabs

Objectives: Several T-cell engaging multispecifics have been supporting by quantitative systems pharmacology models in the past that included a growing number of mechanisms (immune synapse, cytokine release etc.) [1]. In view of recent regulatory commitment to reducing animal testing [2] for biologics there is a growing need for new approach methodologies (NAMs) allowing for surrogate and model-based prediction of the potential safety liabilities as early as possible in the development. While PBPK is widely acknowledged as NAM for exposure, integrated PBPK and T-cell engager QSP models (e.g. [3]) are still scarce. Model complexity and hard-to-automate workflows still limit the integration task. We therefore aim at establishing a cross-platform, two-tiered approach to develop, integrate, and re-use QSP models, exemplified for a bispecific T-cell engager, and using open-source tools.

Methods: We developed two modular frameworks in parallel: a minimal PBPK (mPBPK) QSP model in Tellurium/SBML [4,5], and a whole-body PBPK model constructed using the Open Systems Pharmacology [6] Suite (PK-Sim/MoBi). Both were parameterized using published data for CD3xBCMA and CD3xCD20 T-cell engagers. We then tested procedures to integrate a cytokine release (e.g. [7]) and cytopenia module (e.g. [8]) in the model and calibrate it with published clinical data. After integration with the PBPK framework, we then compare the use of both setups for the execution of a typical PBPK and QSP task, on the example of assessing IL6-dependent DDI liabilities and cytopenia liabilities.

Results: Both the Tellurium and the current OSP version support modularity but modules lack full cross-platform compatibility per se. To bridge this gap, we successfully integrated Tellurium modules into MoBi using a semi-automated LLM-powered approach combined with custom conversion to XML format compatible with MoBi. Qualitatively, both versions of the model can reproduce PK/PD and safety-related information, such as CRS and cytopenia incidence, mitigated by step-up dosing and regimen switch from every week to every other week. When integrated with a PBPK and DDI simulation framework, the model enables a mechanistic exploration of how bsTCE regimen impact the exposure of CYP3A4 substrates. The integration with the cytopenia model allows for linking FcRn affinity–neutropenia relationships for the design of new modalities, especially for targets expressed in the bone marrow.

Conclusions: Automated and modular workflows offer leveraging the “platform” and “fit-for-purpose” aspects of QSP modeling. Through prototyping modules in a scripted environment and integration/re-use of lead QSP modules in extended PK-Sim PBPK models, a large variety of safety questions can be addressed, which otherwise are not addressable under one umbrella. Emphasis on open-source tools renders this approach accessible and fosters the convergence of different modeling communities.

Citations: [1]. Qi, T., Liao, X. & Cao, Y. Development of bispecific T cell engagers: harnessing quantitative systems pharmacology. Trends in Pharmacological Sciences 44, 880–890 (2023).
[2]. FDA. Roadmap to Reducing Animal Testing in Preclinical Safety Studies. (2025).
[3]. Susilo, M. E. et al. Whole-Body Physiologically Based Pharmacokinetic Modeling Framework for Tissue Target Engagement of CD3 Bispecific Antibodies. Pharmaceutics 17, 500 (2025).
[4]. Choi, K. et al. Tellurium: An extensible python-based modeling environment for systems and synthetic biology. Biosystems 171, 74–79 (2018).
[5]. Keating, S. M. et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology 16, e9110 (2020).
[6]. Lippert, J. et al. Open Systems Pharmacology community - an open access, open source, open science approach to modeling and simulation in pharmaceutical sciences. CPT Pharmacometrics Syst Pharmacol (2019) doi:10.1002/psp4.12473.
[7]. Chen, X., Kamperschroer, C., Wong, G. & Xuan, D. A Modeling Framework to Characterize Cytokine Release upon T‐Cell–Engaging Bispecific Antibody Treatment: Methodology and Opportunities. Clinical Translational Sci 12, 600–608 (2019).
[8]. Friberg, L. E. & Karlsson, M. O. Mechanistic Models for Myelosuppression. Invest New Drugs 21, 183–194 (2003).

Keywords: PBPK, QSP, Cytopenia, Safety, DDI, IL6