# AgentDrug: Utilizing Large Language Models in An Agentic Workflow for Zero-Shot Molecular Editing

arXiv: https://arxiv.org/abs/2410.13147 · HTML: https://mlsanity.com/paper/2410.13147/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 9 of its 36 references that are in the map.
- First posted on arXiv 17 Oct 2024.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 9 of 9)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [From Words to Watts: Benchmarking the Energy Costs of Large Language Model Inference](https://mlsanity.com/paper/2310.03003/) (2023)
- [MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter](https://mlsanity.com/paper/2310.12798/) (2023)
- [Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective](https://mlsanity.com/paper/2306.06615/) (2023)
- [Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language](https://mlsanity.com/paper/2303.03363/) (2023)
- [ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining](https://mlsanity.com/paper/2405.14225/) (2024)

## Built on by (most cited first, 3 of 3)

- [Empowering Real-World: A Survey on the Technology, Practice, and Evaluation of LLM-driven Industry Agents](https://mlsanity.com/paper/2510.17491/) (2025)
- [Agentic Molecular Recovery via Molecule-Aware Exploration](https://mlsanity.com/paper/2606.05847/) (2026)
- [Molecular LLM Agents: From Architectural Design to Scientific Autonomy](https://mlsanity.com/paper/2608.23104/) (2026)

## Abstract (arXiv)

Molecular editing-modifying a given molecule to improve desired properties-is a fundamental task in drug discovery. While LLMs hold the potential to solve this task using natural language to drive the editing, straightforward prompting achieves limited accuracy. In this work, we propose AgentDrug, an agentic workflow that leverages LLMs in a structured refinement process to achieve significantly higher accuracy. AgentDrug defines a nested refinement loop: the inner loop uses feedback from cheminformatics toolkits to validate molecular structures, while the outer loop guides the LLM with generic feedback and a gradient-based objective to steer the molecule toward property improvement. We evaluate AgentDrug on benchmarks with both single- and multi-property editing under loose and strict thresholds. Results demonstrate significant performance gains over previous methods. With Qwen-2.5-3B, AgentDrug improves accuracy by 20.7% (loose) and 16.8% (strict) on six single-property tasks, and by 7.0% and 5.3% on eight multi-property tasks. With larger model Qwen-2.5-7B, AgentDrug further improves accuracy on 6 single-property objectives by 28.9% (loose) and 29.0% (strict), and on 8 multi-property objectives by 14.9% (loose) and 13.2% (strict).