Training Chemical Plausibility-Aware Large Language Models for Single-Step Retrosynthesis

Synthesis planning aiming to find pathways of reactions for a target molecule is one of the most important and challenging tasks in drug discovery. Recent progress has produced both specialized deep-learning retrosynthesis systems and general-purpose large language models, but objective comparison remains difficult due to the lack of flexible, chemically interpretable benchmarking protocols. In the current study, we are introducing the URSA (Utilitarian RetroSynthesis Assessment) evaluation framework that provides the opportunity to benchmark the synthetic routes not only from a formal perspective, such as convergence to commercially available starting materials, but also from a chemical plausibility perspective, mimicking the way expert chemists evaluate the reactions and routes. The study covers a comprehensive evaluation of both conventional end-to-end retrosynthesis solutions and LLMs for the synthesis planning task on a set of novel, diverse target molecules with undisclosed synthetic routes, which represent realistic tasks in the daily drug design routine. We find that while LLMs can support high-level strategic planning, they currently underperform specialized retrosynthesis models in reliably solving synthesis planning tasks.

Retrosynthesis prediction aims to identify reactants that can synthesize a given product molecule. Although molecular large language models (LLMs) have recently shown promising results, most existing methods either generate reactants directly or provide only generic product-level analysis, without explicitly reasoning about bond-disconnection strategies that justify specific reactant choices. This paper proposes RetroReasoner, a retrosynthetic reasoning model that captures chemists' strategic disconnection-based thinking. RetroReasoner is trained with supervised fine-tuning and reinforcement learning. For supervised fine-tuning, SyntheticRetro generates structured disconnection rationales paired with reactant predictions. For reinforcement learning, a round-trip reward evaluates predicted reactants by passing them through a forward synthesis model and rewarding predictions that reconstruct the original product. RetroReasoner can also be applied to multi-step retrosynthetic planning by incorporating it into a parallelized Monte Carlo tree search framework, reducing search time while increasing the number and diversity of valid synthetic pathways. Experimental results show that RetroReasoner outperforms prior baselines, including not only molecular LLMs but also retrosynthesis-specific expert models, and generates a broader range of feasible reactant proposals, especially for challenging reaction instances. The code is available at https://github.com/KU-AGI/RetroReasoner.

Multi-step retrosynthesis planning is often considered solved once a route to purchasable starting materials is found, but such a route should also be practical in real-world chemistry. Recent LLM-based planners formulate this process as sequential decision-making over an AND-OR graph, yet typically expand a single molecule per turn and are optimized for solvability alone, leaving alternative routes uncompared across the multiple objectives that determine practicality before the search budget is committed. We introduce RetroPlanner, an LLM-based planner that jointly compares multiple routes to steer the search toward higher synthesizability, as measured by reaction plausibility, round-trip consistency, and starting-material price. RetroPlanner is trained to reason over chemical evidence: structural progress from the target molecule, bond changes and reaction classes, where candidate routes diverge from one another, and how they rank across multiple objectives. Experiments on multi-step retrosynthesis benchmarks demonstrate that RetroPlanner recovers more alternative routes than prior LLM-based planners while improving synthetic route quality and maintaining a high success rate.