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Strategy-first synthesis planning for complex natural products

arXiv cs.MA LLM Agents Daniel Armstrong, Xuan-Vu Nguyen, Octavian Susanu, Gabriel Gibberd, Théo A. Neukomm, Taddäus Strunden, Dan Forster, Morgane Delattre, Shawn Teh, Clément Rols, John Federice, Hayden Leatherwood, M. Lavelle Barnes, Maarten R. Dobbelaere, Peter Wipf, Jon T. Njardarson, Jieping Zhu, Philippe Schwaller 2026-08-07
Representative image for Strategy-first synthesis planning for complex natural products

TL;DR - SynthEx is an LLM-based agentic framework that plans retrosynthetic routes to complex natural products that conventional, catalogue-driven design algorithms cannot handle, and expert chemists rated its key steps comparable to published human syntheses in blinded assessment.

  • Frames the gap in existing tools: they are tuned to catalogued reaction benchmarks and report near-complete success there, but falter on densely functionalized, polycyclic natural products where inventive chemistry is least represented in the record.
  • The agent proposes competing strategies, composes routine plus key steps into a cohesive route, then critiques and revises its own designs — a strategy-first rather than step-by-step search approach.
  • Reported route characteristics: more convergent than existing tools' output, and covering a region of reaction space catalogue-based methods cannot reach.
  • Releases SynthAtlas, an open interactive database of routes to 1,000+ natural products, targeting molecules lacking existing literature routes.

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