Project
AA1-19
Drug Candidates as Pareto Optima in Chemical Space
Project Heads
Konstantin Fackeldey, Christof Schütte, Vikram Sunkara, Jörg Rademann, Marcus Weber, Stefanie Winkelmann
Project Members
Christopher Secker
Project Duration
01.01.2024 − 31.12.2025
Located at
ZIB
Description
Finding drug candidates with mild side effects leads to a multiobjective optimization problem (MOOP) in chemical space. An AI-based generative model will provide possible drug candidates beyond yet known chemical substances. The convergence of respective MOOP solvers will be re-framed.
Related Publications
- Gorgulla, C., …, Secker, C., …, Fackeldey, K. et al. Adaptive Virtual Screening Platform for AI-Driven Ligand Discovery to Explore Ultra-large Chemical Space, Accepted for publication in Nature Biotechnology (2026)
- N. Auevechanichkul. Adaptive steering of multi-agent molecular generators for drug discovery, (Master thesis) Supervisor: C. Secker; Examiners: K. Fackeldey and D. Groth (2026)
- C. Secker, P. Secker, F. Yergöz, M. Celik, S. Chewle, M. Phuong Nga Le, M. Massoud, S. Christgau, M. Weber, C. Gorgulla, A. Nigam, R. Pollice, C. Schütte, and K. Fackeldey. Evolutionary Exploration of Drug-like Chemical Space Utilizing Generative AI and Virtual Screening. bioRxiv, (2026). http://dx.doi.org/10.64898/2026.03.26.714527
- M. Silva, O. ,…, C. Secker,… M. Schapira. CACHE Challenge 4: Targeting the TKB Domain of the E3 ligase CBLB, an Immuno-Oncology Target. ChemRxiv, July 2026. http://dx.doi/org/10.26434/chemrxiv.15005792/v2
- K.Fackeldey, A. Kannan, S. Pokutta, K. Sharma, D. Walter, A. Walther, and M. Weiser. Mathematical optimization for machine learning: Proceedings of the Math+ Thematic Einstein Semester 2023. Proceedings of the MATH+ Thematic Einstein Semester 2023, 2025. URL: http://dx.doi.org/10.1515/9783111376776
- Coomber, C. , Chewle, S., Secker, C. ,Fackeldey, K., Weber, M., Winkelmann, S., Schütte, C. and Sunkara, V. Investigating Endogenous Opioids Unravels the Mechanisms Behind Opioid-Induced Constipation, a Mathematical Modeling Approach, International Journal of Molecular Sciences, 26 (13), (2025), http://dx.doi.org/10.3390/ijms26136207
- Bauer, W. , Galtung, W. , Geserick, P. , Friedrich, K., Weber, M. et al, Pentraxin-3, MyD88, GLP-1, and PD-L1: Performance assessment and composite algorithmic analysis for sepsis identification, Journal of Infection, 91(2), p. 106599 (2025), http://dx.doi.org/10.1016/j.jinf.2025.106599
- Trepte, P., Secker, C. et al AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor, Molecular Systems Biology 20, 4 (2024), https://doi.org/10.1038/s44320-024-00019-8
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