AA1 – Mechanisms of Life

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.

External Website

https://www.zib.de/research/projects/aa1-19-drug-candidates-pareto-optima-chemical-space

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  (2026)
• 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
• Secker, C., Fackeldey, K., Weber, M. et al. Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists. J Cheminform 15, 85 (2023). https://doi.org/10.1186/s13321-023-00746-4
• Ray S, Fackeldey K, Stein C, Weber M. Coarse-Grained MD Simulations of Opioid Interactions with the μ-Opioid Receptor and the Surrounding Lipid Membrane. Biophysica. 2023; 3(2):263-275. https://doi.org/10.3390/biophysica3020017
• Donati, L., Fackeldey, K. & Weber, M. Augmented ant colony algorithm for virtual drug discovery. J Math Chem 62, 367–385 (2024). https://doi.org/10.1007/s10910-023-01549-6
• Gorgulla C, Nigam AK, Koop M, Çınaroğlu SS, Secker C, […], Fackeldey K et al. VirtualFlow 2.0 – The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules. bioRxiv (2023). https://doi.org/10.1101/2023.04.25.537981

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