Enabling multi-target drug discovery through latent evolutionary optimization and synthesis-aware prioritization (EVOSYNTH)

Complex diseases, such as cancer and neurodegeneration, feature interconnected pathways, making single-target therapies ineffective due to pathway redundancy and compensatory mechanisms. Polypharmacy, which combines multiple drugs to target distinct proteins, addresses this but often leads to drug-drug interactions, cumulative toxicity, and complex pharmacokinetics. To overcome these challenges, we introduce EVOSYNTH, a modular framework for multi-target drug discovery that combines latent evolution and synthesis-aware prioritization to generate and prioritize candidates with high translational potential. Latent evolution navigates a chemically and functionally informed latent space to identify candidates with strong predicted affinity across multiple targets. Synthesis-aware prioritization evaluates both retrosynthetic feasibility and the trade-off between synthetic cost and therapeutic reward, enabling practical and efficient candidate selection. Applied to dual inhibition of JNK3 and GSK3β in Alzheimer’s disease and PI3K and PARP1 in ovarian cancer, EVOSYNTH consistently outperforms baseline generative models, achieving higher predicted affinities, improved scaffold diversity, and lower synthesis costs. These findings highlight EVOSYNTH’s ability to integrate target-driven generation with practical synthesizability, establishing a scalable framework for multi-target and polypharmacological drug discovery. Our source code and data to reproduce all experiments are publicly available on GitHub at: https://github.com/HySonLab/EvoSynth. Complex diseases such as cancer and neurodegeneration involve interconnected biological pathways that limit the effectiveness of single-target therapies. Here, the authors introduce EVOSYNTH, a synthesis-aware multi-target drug discovery framework that integrates latent evolutionary optimization with retrosynthetic prioritization and demonstrates its ability to generate potent and experimentally actionable candidates through representative case studies in Alzheimer’s disease and ovarian cancer.